Population genetics | Egypt | Ancient DNA
Are the Copts the true descendants of the pharaohs?
Egypt's Christians have long called themselves the last true Egyptians. We compared Copts and Muslim Egyptians with the genomes of ancient Egyptians, from an Old Kingdom man to the mummies of Abusir el-Meleq. The Copts are the closest living population to the ancient Egyptians in our data. But they are not the only heirs.
Hero image: AI generated illustration of a Coptic village built in the courtyard of an old pharaonic temple in Upper Egypt, around 550 AD, a century before the Arab conquest. Clothing, buildings and the scene are approximations, and it is not a reconstruction of the individuals whose genomes are discussed here.
The word Copt comes, through Arabic, from the Greek word for Egyptian. The Coptic language, still used in the liturgy of the Coptic Church, is the last stage of the language of the pharaohs. And many Copts see themselves as the direct descendants of the ancient Egyptians, a people who kept their blood as they kept their faith, while the rest of Egypt mixed with Arab conquerors. Is that true? For the first time, ancient genomes from Egypt allow the question to be tested.
We used the three ancient Egyptian genomes available in Global25, a man buried at Nuwayrat around 2700 BC and two people from Abusir el-Meleq dated to around 650 BC, and compared them with two samples of Copts and 74 Muslim Egyptians from nine governorates. The answer is clear on one point and more nuanced on another.
What ancient DNA says about the ancient Egyptians
Egypt's climate destroys DNA, and the first genomes came late. In 2017, Verena Schuenemann and colleagues sampled 151 mummies from Abusir el-Meleq in Middle Egypt, dated from the New Kingdom to the Roman period (1388 BC to 426 AD). They recovered 90 mitochondrial genomes and genome-wide data from three individuals. The ancient Egyptians of Abusir el-Meleq were most closely related to ancient populations of the Near East, and the community showed no major genetic shift over 1,300 years, despite Persian, Greek and Roman rule. Present-day Egyptians, by contrast, share about 8% more ancestry with sub-Saharan Africans, which the authors attributed to gene flow within the last 1,500 years, including the trans-Saharan slave trade.
In 2025, Adeline Morez Jacobs and colleagues published the first complete ancient Egyptian genome, from a man buried in a pottery vessel in a rock-cut tomb at Nuwayrat, radiocarbon dated to 2855 to 2570 BC, at the dawn of the Old Kingdom. About 80% of his ancestry traced to Neolithic North Africa, and about 20% to the eastern Fertile Crescent, including Mesopotamia. No sub-Saharan ancestry was detected. The authors stress that he is a single individual.
In 2026, the Egypt Genome Project sequenced 1,024 Egyptians from 21 governorates. In its preprint, Egyptians share most of their ancestry with Middle Eastern populations, 71.8%, but carry an Egypt-specific component of 18.5% that sets them apart from their neighbours. That study did not separate Christians and Muslims, nor did it use ancient genomes.
Who are the Copts in the genetic data?
The Coptic samples available to us come, as far as we can tell, from Sudan. In 2015, Begona Dobon and colleagues genotyped Copts living in Sudan, an example of recent migration from Egypt, and kept 27 after quality control. The Copts formed their own genetic component, close to North African and Middle Eastern populations, and the authors suggested that they could resemble the ancestral Egyptian population, a remnant of North Africans before the migrations of Arabs from Arabia. In 2017, Nina Hollfelder and colleagues sampled another group of Sudanese Copts, whose ancestors arrived about 200 years ago. They found a strong affinity with Egyptians, very low differentiation from them, and only low levels of admixture with local Sudanese since their arrival.
Our two Coptic averages, of 27 and 11 people, most likely come from these Sudanese samples. They are only 9.7 units apart in Global25, which makes them a good check on each other. Our 74 Muslim Egyptians come from nine governorates, all in Lower Egypt: the Nile Delta, Cairo, Giza and Alexandria. This matters, and we come back to it below.
The closest living people to the mummies
We first measured the Global25 distance from each present-day population to the Late Period Egyptians of Abusir el-Meleq and to the Old Kingdom man of Nuwayrat. The Copts come first on both: 40 and 42 units from the Late Period Egyptians, closer than any of the hundreds of populations we tested. Next come the Yemenis (48) and the Saudis of Jizan (52), whose mixture of Near Eastern and East African ancestry happens to land close to the ancient Egyptians. The Muslim Egyptians of the Delta and Cairo are further away, 73 to 86, behind Palestinians and Sinai Bedouins. Among ancient genomes, two outliers sit even closer than the Copts: one person buried in Iron Age Beirut and one in Roman Britain, whose profiles look Egyptian. They are reminders that Egyptians travelled across the ancient Mediterranean world.
The Old Kingdom man tells a slightly different story. He is further from everyone, as expected for a genome 2,000 years older from another site, and he is relatively closer to North Africans: a Tunisian Arab group from R'Baya is as close to him as the Copts (54.5 against 52.9 and 54.6), and Libyans sit at 78 from him but 98 from the Late Period Egyptians. This fits his large North African Neolithic ancestry.
How much ancient Egyptian ancestry?
We then modelled each population as a mixture of Late Period Egyptians and three sources that could have arrived later: the Levant (Lebanese Christians), Arabia (Saudis of Najd) and sub-Saharan Africa (Dinka). In this main model, the Copts are 70 to 75% Late Period Egyptian, with 7 to 12% Levant-related, 12 to 13% Arabian-related and 6% sub-Saharan ancestry. The Muslim Egyptians are 42% Late Period Egyptian, with 35% Levant-related, 10% Arabian-related and 13% sub-Saharan ancestry. By governorate, their Egyptian share ranges from 28% in Gharbia to 57% in Beheira, and the samples are small.
The sub-Saharan difference matches the literature. The Late Period Egyptians themselves need almost none, the Copts about 6% and the Muslim Egyptians about 13%: an average close to the 8% increase that Schuenemann and colleagues measured in present-day Egyptians. The Arabian-related share is more surprising: it is not higher in Muslims than in Copts. In Global25, the Arabian and Levantine sources are close, and part of the Arabian signal in the Copts may reflect older contacts across the Red Sea or the limits of an ancient source made of two genomes of modest coverage.
When we model the Muslim Egyptians directly from the Copts, the best fit (7.6) adds Levant-related (32%), Maghrebi (11%), Arabian (13%) and sub-Saharan (10%) ancestry to a Coptic base of 35%. These numbers should not be read as "only a third Egyptian": the Levantine and Arabian proxies overlap heavily with ancient Egyptian ancestry itself. What they show is the direction of the difference. Muslim Egyptians of the Delta and Cairo received more ancestry from the Levant, the Maghreb, Arabia and sub-Saharan Africa, the regions that sent Arab tribesmen, Fatimid armies from Ifriqiya, Bedouin migrants and enslaved Africans into Egypt over thirteen centuries. The Copts, a religious minority that married within the community, received less of it.
The Near Eastern layer is older than Islam
A common assumption is that any Near Eastern ancestry in Egyptians came with the Arab conquest of 639 to 642. The ancient genomes say otherwise. Modelled from the Old Kingdom man of Nuwayrat, the Late Period Egyptians of Abusir el-Meleq already carry about 42% Levant-related ancestry. The Copts carry almost exactly the same share, 41%, with 4% sub-Saharan and 3% Arabian ancestry. Their Near Eastern layer is, for the most part, pharaonic. The Muslim Egyptians carry 52% Levant-related and 12% sub-Saharan ancestry on the same scale.
This comparison has limits: it relies on one Old Kingdom genome and two Late Period genomes, from different places in Middle Egypt, two thousand years apart. It does not tell when the Near Eastern ancestry arrived between the Old Kingdom and the Late Period, or whether it was already present in other parts of Old Kingdom Egypt. But it fits Schuenemann and colleagues' finding that the people of Abusir el-Meleq were closest to the ancient Near East, long before Islam.
Testing the result
Ancient genomes of low coverage give noisy Global25 coordinates: the two Late Period individuals are 39 units apart, partly for that reason. We therefore tested how far our conclusion depends on our choices.
First, we changed every source. We swapped the Arabian proxy (Najd Saudis, all Saudis, Yemenis, Sinai Bedouins), the sub-Saharan proxy (Dinka, Nubians, Christian Nubians of Kulubnarti, the 4,500 year old Ethiopian of Mota), the Levantine proxy (Lebanese and Palestinian Christians, Late Bronze Age Jordanians, Roman era Lebanese) and the ancient Egyptian source (the Late Period average or one genome alone). Across all 128 combinations, the Copts always carry more Late Period Egyptian ancestry than the Muslim Egyptians, by 10 to 56 points, with a median of 35. The individual percentages move a lot, especially with mixed sub-Saharan proxies like the Nubians; the ranking never does.
Second, we added random noise to the ancient Egyptian source, of 10, 20 and 30 units, 200 times each. The gap between Copts and Muslims shrinks a little as noise grows, from 27 to 21 points at the median, but even at the highest noise level it stayed above 16 points in 95% of runs, and it never fell below 10 in any of the 600 runs. Third, we checked that the model recovers known mixtures: Late Period Egyptian profiles spiked with 5 to 30% of Arabian, Levantine or Dinka ancestry were recovered exactly, and adding 10% of Arabian ancestry to the Coptic profile raised the Arabian share by the expected amount.
So, are the Copts the descendants of the pharaohs?
Yes, more directly than any other living population in our data. Of all the present-day populations we tested, the Copts are the closest to the ancient Egyptians of Abusir el-Meleq and to the Old Kingdom man of Nuwayrat, and the most simply modelled from them. Their religious endogamy, over thirteen centuries as a minority, kept much of the ancient Egyptian gene pool intact.
But the Copts are not the only heirs, and they are not a frozen population. Muslim Egyptians also descend largely from the ancient Egyptians: the Arab conquest brought a new religion and, slowly, a new language, but no population replacement. What separates the two communities is a few centuries of additional gene flow into the Muslim majority, from the Levant, the Maghreb, Arabia and sub-Saharan Africa. And the Copts themselves carry about 6% of recent sub-Saharan ancestry and a Near Eastern layer that dates back to pharaonic times.
Some limits should be stated. Our Coptic samples are Copts of Sudan, descended from 19th century migrants from Egypt, probably from Upper Egypt; our Muslim samples come only from Lower Egypt. Part of the difference may therefore be geographic, between the south and the more cosmopolitan Delta, rather than religious. Muslim Egyptians from Upper Egypt, and Copts sampled in Egypt itself, are needed to settle this. The ancient genomes are few, of modest coverage, and come from Middle Egypt only. And our outside sources are present-day proxies for populations that mixed long ago.
Key points
- The Copts are the closest living population to the ancient Egyptians in Global25: 40 units from Late Period Egyptians, against 73 to 86 for Muslim Egyptians of Lower Egypt.
- In our main model, Copts are about 70% Late Period Egyptian and Muslim Egyptians about 42%; across 128 versions of the model, the Copts always score higher, by a median of 35 points.
- Muslim Egyptians carry more Levant-related, Maghrebi and sub-Saharan ancestry (13% against 6%), consistent with centuries of gene flow into the Delta and Cairo after the Arab conquest.
- Most of the Near Eastern ancestry of the Copts predates Islam: Late Period Egyptians already carried about 42% Levant-related ancestry relative to the Old Kingdom man of Nuwayrat.
- Muslim Egyptians are also heirs of ancient Egypt: the conquest changed religion and language, not the population.
- All Coptic samples come from Sudan and all Muslim samples from Lower Egypt, so part of the difference may be regional.
Global25 coordinates used in this article
Copts, Muslim Egyptians by governorate, the ancient Egyptian genomes and the outside sources. They can be pasted directly into the Vahaduo tool.
Copts_avg27,0.017729,0.142455,-0.049604,-0.104384,-0.000371,-0.043313,-0.014851,-0.002682,0.046742,-0.000362,0.007449,-0.012015,0.028901,0.002011,0.000624,0.001569,-0.003961,-0.001525,-0.003607,0.004888,0.001147,0.000706,0.000571,0.002179,-0.000501
Copts_avg11,0.015418,0.144574,-0.047209,-0.105827,0.000923,-0.043786,-0.013588,-0.004951,0.049513,-0.003115,0.008252,-0.012180,0.029840,0.003628,-0.002208,-0.001302,-0.007112,-0.001129,-0.003805,0.004252,-0.000306,0.001248,0.003563,0.003440,-0.003396
Egyptian_Muslims_avg74,-0.020893,0.134029,-0.042424,-0.084544,-0.004164,-0.032185,-0.013353,-0.000132,0.036472,-0.000461,0.006568,-0.009880,0.021547,0.000424,0.000264,0.001747,-0.001368,-0.002936,-0.003867,0.003126,-0.000623,-0.000660,0.001811,0.002086,-0.000196
Egyptian_Muslims_Alexandria,-0.016163,0.132434,-0.040729,-0.082489,-0.001662,-0.033746,-0.014148,-0.003646,0.035942,0.001713,0.005419,-0.011690,0.021021,-0.001321,-0.003502,0.000610,0.003416,-0.003421,-0.005605,0.002501,-0.000873,0.000692,0.000419,0.005615,0.002347
Egyptian_Muslims_Cairo,-0.016504,0.133034,-0.041389,-0.079135,-0.002616,-0.032421,-0.012867,0.000519,0.035587,0.000046,0.000690,-0.009741,0.019846,-0.002340,-0.001832,0.008652,0.006813,-0.005162,-0.004368,0.005503,-0.002153,-0.002350,0.004714,0.005091,-0.002694
Egyptian_Muslims_Dakahlia,-0.009485,0.132780,-0.041515,-0.088717,-0.006155,-0.034559,-0.013729,-0.000635,0.036490,0.000851,0.006265,-0.010978,0.024232,-0.000069,-0.000373,-0.002144,-0.002727,-0.002439,-0.003541,0.002991,0.000728,-0.003287,0.001715,0.000914,-0.000499
Egyptian_Muslims_Gharbia,-0.007456,0.128922,-0.044815,-0.085823,-0.004307,-0.035029,-0.003373,-0.005631,0.036072,-0.001758,0.008705,-0.010864,0.026851,0.002888,0.003282,0.005804,-0.009228,-0.003998,-0.002455,0.003224,0.001435,0.000791,0.003113,-0.000517,0.000476
Egyptian_Muslims_Sharqia,-0.018792,0.135647,-0.045216,-0.087915,-0.006729,-0.040155,-0.007246,-0.002531,0.042865,-0.007338,0.004053,-0.013569,0.026231,0.002610,-0.000498,0.004192,-0.003337,-0.000578,0.000742,0.004251,0.004254,0.002370,-0.001967,-0.001933,-0.001397
Egyptian_Muslims_Beheira,-0.017317,0.134920,-0.042345,-0.090625,-0.004286,-0.034483,-0.012153,0.001648,0.038699,-0.000104,0.006171,-0.008424,0.020760,-0.002703,-0.001115,-0.003826,-0.006920,-0.007203,-0.005163,0.003332,-0.004243,0.000000,0.003495,-0.000249,-0.000257
Egyptian_Muslims_Giza,-0.025611,0.135065,-0.042614,-0.087856,0.002616,-0.033606,-0.013631,-0.003346,0.040291,0.000820,0.007633,-0.007718,0.025272,0.001307,0.005090,0.008552,0.002543,-0.004371,-0.005719,0.002001,0.001685,0.000804,0.007025,0.000964,0.000179
Egyptian_Muslims_Qalyubia,-0.022765,0.132019,-0.041483,-0.084949,-0.000923,-0.028865,-0.020328,-0.002769,0.033440,0.003371,0.009987,-0.011765,0.022671,-0.002959,0.002240,-0.008884,-0.016037,-0.003864,-0.003268,-0.002501,-0.002870,-0.004080,0.004313,0.002350,0.000539
Egypt_LatePeriod_Abusir_avg2,0.050082,0.146744,-0.042426,-0.118380,-0.002001,-0.049782,-0.015628,-0.004731,0.047449,0.006196,0.009012,-0.011465,0.029732,-0.005849,-0.000815,-0.002056,-0.007431,-0.001963,-0.003520,0.012006,0.005615,0.001669,0.003635,0.003916,-0.000598
Egypt_TIP_JK2911,0.056912,0.143190,-0.046009,-0.116281,-0.003385,-0.045738,-0.019271,-0.002538,0.044382,0.007472,0.015427,-0.012139,0.032557,-0.010046,-0.001900,0.001989,-0.003912,0.001394,-0.007542,0.013757,0.004617,0.001113,0.002958,-0.002169,-0.006706
Egypt_TIP_JK2134,0.048944,0.149283,-0.038466,-0.123064,0.004616,-0.048248,-0.007520,-0.003461,0.048268,0.010570,-0.001624,-0.008692,0.031813,0.000826,-0.001493,-0.009679,-0.013038,-0.005321,-0.004399,0.005378,0.004367,0.001484,0.002958,0.010363,0.006826
Egypt_OldKingdom_Nuwayrat_NUE001,0.011382,0.129988,-0.043746,-0.122095,0.008925,-0.052710,-0.029141,-0.006000,0.078128,-0.005832,0.008607,-0.017984,0.044152,0.000000,0.006650,0.009546,-0.003260,-0.007348,-0.010559,0.023761,0.002496,-0.002844,0.009860,0.012532,-0.003832
Lebanese_Christian,0.090510,0.145221,-0.051945,-0.080260,-0.014396,-0.027776,-0.000923,-0.004957,0.003568,0.009166,0.005323,-0.004935,0.010891,0.001315,-0.008716,0.006654,-0.002260,0.001492,0.002956,-0.000509,-0.000573,0.000691,-0.002027,0.002575,0.000430
Saudi_Najd,0.057951,0.136946,-0.062343,-0.106186,-0.013198,-0.043738,-0.013242,-0.008778,0.047379,-0.006565,0.013764,-0.028491,0.058585,0.003792,0.004316,0.023631,-0.024332,0.005910,-0.001087,0.024357,0.009158,0.014435,-0.005341,0.006490,-0.006394
Dinka,-0.577601,0.053054,0.001211,-0.008026,-0.003022,-0.002392,-0.013324,0.015908,0.079653,-0.098794,-0.020397,0.023579,-0.041837,-0.000113,0.008851,-0.017184,0.019648,-0.011905,0.021068,-0.020498,0.000760,0.003432,-0.004037,-0.001807,0.005784
Berber_Morocco_Central_Atlas,-0.049432,0.137822,-0.003664,-0.073875,0.030071,-0.033945,-0.026825,0.010087,0.073716,0.030798,0.005846,-0.006573,0.019475,-0.018756,0.022646,-0.020078,-0.003092,-0.024017,-0.052093,0.007664,-0.018058,-0.047359,0.030002,-0.003150,0.007544
Saudi_all,0.052090,0.140143,-0.060483,-0.111449,-0.010307,-0.045575,-0.012521,-0.008698,0.052667,-0.006099,0.015309,-0.029382,0.058034,0.005754,0.003958,0.023486,-0.022397,0.005200,-0.000856,0.025372,0.010450,0.014695,-0.005302,0.005351,-0.006820
Yemeni_Dhamar,0.034602,0.140549,-0.058944,-0.110564,-0.009509,-0.047105,-0.013043,-0.008469,0.049515,-0.008273,0.014095,-0.025687,0.048538,0.005285,0.003787,0.015699,-0.014094,0.004827,0.000063,0.017408,0.009633,0.011920,-0.005596,0.004591,-0.003964
Saudi_Jizan,0.040976,0.139381,-0.057794,-0.109336,-0.011310,-0.043298,-0.009165,-0.007211,0.050620,-0.005786,0.013763,-0.024578,0.052329,0.007466,0.002952,0.020651,-0.020209,0.008203,0.001603,0.017321,0.006645,0.009521,-0.006809,0.004759,-0.002485
Bedouin_Sinai,0.001465,0.131946,-0.041839,-0.084474,-0.000642,-0.032339,-0.011248,0.001160,0.033946,-0.001682,0.009739,-0.008511,0.027699,0.002149,0.002720,0.007327,-0.011273,0.007131,-0.014383,0.005158,0.001838,0.007524,0.002754,0.003735,0.000089
Palestinian_Christian,0.084785,0.146595,-0.053306,-0.085641,-0.012179,-0.031584,-0.002395,-0.004245,0.007998,0.010400,0.007851,-0.007854,0.014453,0.001319,-0.006834,0.005443,-0.001491,0.004436,0.002578,-0.000943,-0.000389,0.002758,0.000058,0.002833,-0.000982
Jordan_LBA_Baqah,0.087786,0.150044,-0.059915,-0.102068,-0.010156,-0.037267,-0.006786,-0.010586,0.014700,0.009727,0.010291,-0.009292,0.022801,0.000086,-0.009212,0.016226,0.002168,0.003151,0.002467,0.006831,0.004071,0.007048,-0.008165,0.000421,-0.001078
Lebanon_Roman,0.087359,0.146998,-0.056379,-0.087210,-0.009925,-0.029005,-0.006580,-0.007442,0.008897,0.015718,0.002152,-0.010866,0.012227,-0.000103,-0.009840,0.009613,0.002803,-0.000950,0.001257,0.003877,0.000530,0.004606,-0.002188,-0.002380,-0.005927
Sudan_Kulubnarti_Christian_avg,-0.211975,0.109484,-0.029836,-0.078044,0.002566,-0.034260,-0.023825,0.009570,0.084832,-0.049749,-0.002443,-0.007228,0.008645,0.000378,0.012718,-0.010005,0.007155,-0.010351,0.002263,-0.000721,0.000042,-0.000452,0.001552,-0.002342,-0.001087
Ethiopia_Mota_4500BP,-0.517895,0.040621,-0.003017,-0.000646,-0.002154,-0.009761,0.057813,-0.049383,0.089172,-0.084375,-0.013803,-0.014987,-0.036571,-0.001651,0.023480,-0.030628,0.022817,0.041047,0.005279,-0.008629,0.002620,0.001855,-0.006039,0.001205,0.002515
Nubian_Danagla,-0.238573,0.101045,-0.030396,-0.069219,-0.001570,-0.028224,-0.020258,0.009438,0.081830,-0.052338,-0.005067,-0.001094,0.006749,0.000289,0.009487,-0.008141,0.010144,-0.007981,0.002464,-0.002226,0.001597,-0.000569,-0.000900,0.000205,-0.000323
Libyan_Arab,-0.030189,0.134122,-0.023096,-0.083920,0.011596,-0.035469,-0.021774,0.001983,0.052887,0.013887,0.006975,-0.012952,0.029803,-0.007114,0.008800,0.000836,-0.001374,-0.010478,-0.021804,0.011700,-0.002721,-0.014832,0.010567,-0.000713,0.001238
References
- Ancient DNA Morez Jacobs A, Irish JD, Cooke A, Anastasiadou K, Barrington C, et al. (2025). Whole-genome ancestry of an Old Kingdom Egyptian. Nature 644: 714 to 721. doi.org/10.1038/s41586-025-09195-5
- Ancient DNA Schuenemann VJ, Peltzer A, Welte B, van Pelt WP, Molak M, et al., Schiffels S, Krause J (2017). Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nature Communications 8: 15694. doi.org/10.1038/ncomms15694
- Genomics Dobon B, Hassan HY, Laayouni H, Luisi P, Ricano-Ponce I, et al., Bertranpetit J (2015). The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Scientific Reports 5: 9996. doi.org/10.1038/srep09996
- Genomics Hollfelder N, Schlebusch CM, Gunther T, Babiker H, Hassan HY, Jakobsson M (2017). Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genetics 13(8): e1006976. doi.org/10.1371/journal.pgen.1006976
- Genomics Amer K, et al., Abdel-Ghaffar KA (2026). EGP1K: Whole-genome sequencing of 1,024 Egyptians characterizes population structure and genetic diversity. bioRxiv preprint. biorxiv.org/content/10.64898/2026.04.02.715521v1
- Data Global25 coordinates by Davidski (Eurogenes), and the Moriopoulos Collection 2026 of averages. Admixture models, robustness tests and figures: ExploreYourDNA.