Malagasy DNA
Genetic origins and closest populations · Madagascar · Sub-Saharan Africa
Madagascar was one of the last large landmasses settled by people, and its language tells the story: Malagasy is an Austronesian language whose closest relative, Ma'anyan, is spoken in southern Borneo, across the Indian Ocean. Seafarers from Island Southeast Asia and Bantu-speaking people from East Africa both settled the island, mainly within the last 1,500 years. For an average from the Sofia region in the northwest, our model puts the African side at 44.4% West African and 12.3% Nilotic East African, and the Asian side at 17.4% Southern Chinese Neolithic plus 16.8% Southeast Asian Neolithic farmer, with small forager and other shares. No other African population in our atlas carries an East or Southeast Asian-related share. That uniqueness shows in the neighbours: the four closest modern averages are all from Madagascar, the Vezo (0.0084), Temoro, Toliara and Mikea, and the next, the Siddi of India, is already far (0.1554).
- Largest ancient components in our model: West African 44.4%, Southern Chinese Neolithic farmers 17.4%, Southeast Asian Neolithic farmers 16.8%
- Closest modern population in our data: Madagascar (Vezo), distance 0.0084
- Closest ancient group in our data: Tanzania Late Medieval-Early Modern Kilwa Swahili (Swahili-Mixed Profile), distance 0.1838
Malagasy is one of the 335 modern populations in our population genetics atlas. The numbers on this page describe the average Global25 (G25) genome of the Malagasy individuals sampled in Madagascar, listed in the G25 sheet as "Malagasy_Sofia". Like every population average, it smooths over a lot of variation between individuals.
Ancient make-up of the Malagasy average
Modelled as a mix of deep ancestral reference populations, the Malagasy average comes out as 44.4% West African, 17.4% Southern Chinese Neolithic farmers and 16.8% Southeast Asian Neolithic farmers. The West African component reflects ancestry from sub-Saharan Africa. The Southern Chinese Neolithic farmers share (17.4%) reflects the Neolithic rice and millet farmers of southern China, whose descendants spread into Southeast Asia.
Smaller traces of Western rainforest foragers (BiAka), Anatolian Neolithic farmers, Southern African foragers (San) and South Asian hunter-gatherer related (Irula proxy) (under 5% each) also appear. At that level they can reflect real minor ancestry, but also simple model noise, so they should not be over-read. The fit is acceptable (fit distance 0.036): treat the proportions as a good approximation rather than exact values. This population was modelled with a global set of reference populations (ancient genomes, plus modern stand-ins where no suitable ancient genome exists), because West Eurasian sources alone cannot describe it.
Sankofa – African Ancestry Report
Closest modern populations to Malagasy
Genetically, the Malagasy average sits nearest to Madagascar (Vezo) at 0.008, Malagasy (Temoro) at 0.013 and Malagasy (Toliara) at 0.018. On our scale, a distance of 0.008 counts as very close. Leaving aside the other regional samples listed under the same name in the G25 sheet, the nearest other populations are Madagascar (Vezo) (0.008), Madagascar (Mikea) (0.019) and Siddi (Karnataka) (0.155). By the tenth closest (Shwashin Arab (Tunisia)) the distance grows to 0.204, a common pattern for a population that shares ancestry with its neighbours while keeping a profile of its own.
| # | Population | Distance | Closeness |
|---|---|---|---|
| 1 | Madagascar (Vezo) | 0.0084 | Very close |
| 2 | Malagasy (Temoro) | 0.0125 | Very close |
| 3 | Malagasy (Toliara) | 0.0182 | Very close |
| 4 | Madagascar (Mikea) | 0.0189 | Very close |
| 5 | Siddi (Karnataka) | 0.1554 | Distant |
| 6 | Swahili (Kenya Siyu) | 0.1781 | Distant |
| 7 | Swahili (Kenya Wasini) | 0.1787 | Distant |
| 8 | Swahili (Kenya Faza) | 0.1884 | Distant |
| 9 | Shwashin Berber (East Zenati Tunisia Matmata) | 0.2042 | Distant |
| 10 | Shwashin Arab (Tunisia) | 0.2044 | Distant |
Distances are Euclidean distances between averaged G25 coordinates. On our scale, below 0.025 is very close, below 0.050 close, below 0.080 moderate, and beyond that distant.
Closest ancient populations to Malagasy
Looking back in time, the ancient sample that most resembles the Malagasy average is Tanzania Late Medieval-Early Modern Kilwa Swahili (Swahili-Mixed Profile) (Late Medieval to Early Modern, c. 1300-1800 AD), at 0.184. Kenya Early Modern Mtwapa Swahili and Tanzania Early Modern Songo Mnara Swahili (Swahili-Mixed Profile) come next. Even the best ancient match is distant, so the modern population is better described as a blend of several ancestral sources than as the continuation of one. A close ancient match is not proof of direct descent: it means those individuals carried a similar overall mix of ancestry.
| # | Ancient sample or group | Period | Distance |
|---|---|---|---|
| 1 | Tanzania Late Medieval-Early Modern Kilwa Swahili (Swahili-Mixed Profile) | Late Medieval to Early Modern, c. 1300-1800 AD | 0.1838 |
| 2 | Kenya Early Modern Mtwapa Swahili | Early Modern, c. 1500-1800 AD | 0.2075 |
| 3 | Tanzania Early Modern Songo Mnara Swahili (Swahili-Mixed Profile) | Early Modern, c. 1500-1800 AD | 0.2178 |
| 4 | Kenya Early Modern Kilifi 400BP | c. 1550 AD | 0.2299 |
| 5 | Kenya IA Deloraine | Iron Age | 0.2432 |
| 6 | Kenya Late Medieval-Early Modern Makwasinyi Swahili | Late Medieval to Early Modern, c. 1300-1800 AD | 0.2454 |
| 7 | Spain Andalusia Early Modern (SSA-Mixed Profile) | Early Modern, c. 1500-1800 AD | 0.2491 |
| 8 | Libya N Saharan Pastoral Takarkori | Neolithic | 0.2523 |
| 9 | Kenya Pastoral IA | Iron Age | 0.2593 |
| 10 | Tanzania Early Modern Songo Mnara Swahili (Southern Nilotic Profile) | Early Modern, c. 1500-1800 AD | 0.2598 |
Ancient DNA from Madagascar
Our database lists the ancient DNA studies linked to Madagascar below.
Ancient DNA studies on Madagascar
Compare yourself with Malagasy
Paste your G25 coordinates (scaled, one line, with or without a name in front) and we compute your genetic distance to the Malagasy average and to its closest neighbours, right in your browser. Nothing is uploaded or stored.
| # | Population | Your distance | Closeness |
|---|
This list only covers Malagasy and its neighbours. To find out which of our reports actually fits your DNA, run the free Report Finder: it runs the same fit test that every report uses before an order.
No G25 coordinates yet? Get a free simulated G25 from your raw DNA file, or order G25 coordinates.
About these numbers
Keep in mind that a population average is a statistical summary of a limited number of sampled individuals. Real people inside any group vary, some carry more of one ancestry and some less, and no genetic profile decides who is or is not Malagasy. Use these numbers as a map of deep ancestry, not as a label.
Method: averaged G25 coordinates, Euclidean distances to other modern and ancient averages, and a non-negative least-squares model against deep ancestral reference populations (data generated 2026-10-01). Read the full method.
Go deeper than the average
This page describes the Malagasy average. Your own DNA has its own story: Sankofa – African Ancestry Report (15€) models your genome against the ancient sources and modern communities of the region, era by era, in a personal PDF report.
A report built for people of predominantly Sub-Saharan African (SSA) ancestry: modelling against 230+ regional African populations (West, Central, East & Southern Africa, the Horn of Africa, Madagascar) plus the European, Amerindian and...
More populations from Sub-Saharan Africa
Frequently asked questions
What is the ancient genetic make-up of Malagasy?
Modelled with deep ancestral reference populations, the Malagasy average is about 44.4% West African, 17.4% Southern Chinese Neolithic farmers and 16.8% Southeast Asian Neolithic farmers. These proportions are model estimates for a group average, not exact values for any one person.
Which populations are genetically closest to Malagasy?
Leaving aside other regional samples listed under the same name in the G25 sheet (such as Malagasy (Temoro)), the closest modern populations to the Malagasy average are Madagascar (Vezo), Madagascar (Mikea) and Siddi (Karnataka). The closest ancient matches are Tanzania Late Medieval-Early Modern Kilwa Swahili (Swahili-Mixed Profile), Kenya Early Modern Mtwapa Swahili and Tanzania Early Modern Songo Mnara Swahili (Swahili-Mixed Profile).
Can a DNA test tell me if I am Malagasy?
No DNA test can confirm an ethnicity or a nationality. What DNA can show is how similar your genome is to the sampled Malagasy average and to its neighbours. If you have G25 coordinates, paste them in the comparison box on this page to check that for free.
Which ExploreYourDNA report suits Malagasy ancestry?
Sankofa – African Ancestry Report is the report built for this heritage, and its reference panel fits the Malagasy average closely. Your own DNA may differ from the average, so the free Report Finder checks every report against your file before you buy.
Where does the data on this page come from?
From the averaged Global25 (G25) coordinates of the sampled individuals: genetic distances to other modern and ancient population averages, and a non-negative least-squares model against deep ancestral reference populations. The full method is described at https://www.exploreyourdna.com/populations#method.