The history of Ecuador was marked by the arrival of Europeans with Africans, resulting in the mixture of Native Americans with Africans and Europeans. The present study contributes to the knowledge of the Ecuadorian mestizo population by offering information about ancestry and ethnic heterogeneity. Forty-six AIM-InDels (Ancestry Informative Insertion/Deletion Markers) were used to obtain information on 240 Ecuadorian individuals from three regions (Amazonia, the Highlands, and the Coast). As a result, the population involved a significant contribution from Native Americans (values up to 51%), followed by Europeans (values up to 33%) and Africans (values up to 13%). Furthermore, we compared the data obtained with nine previously reported scientific articles on autosomal, mitochondrial DNA and Y chromosomes. The admixture results correspond to Ecuador’s historical background and vary slightly between regions.

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Ancestry Informative Insertion-Deletion markers have been used as a tool to infer the origin of population. In the present study, we report the results obtained for 46 AIM-INDELS in the Ecuadoŕs highland population by analyzing 171 unrelated individuals. Native American was the most prevalent ancestry in the studied population (63.1%), followed by European (30.3%) and lastly African (6.6%). The admixture found is in agreement with the historical background of Ecuador.

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