Peru is a country with great population diversity. According to the 2017 census conducted by the Instituto Nacional de Estadística e Informática, a total of 55 indigenous peoples were identified (51 from the Amazon and 4 from the Andes highlands). Within this diversity of populations, the majority of Peruvians self-identify as mestizo (around 60% of the population). Among the minority groups, a significant proportion identifies as Aymara (representing 2.4% to 5% of the population). The aim of this investigation was to estimate the proportions of African, European and Native American ancestry in Peruvian Aymara and Mestizo populations, using 46 Insertion/Deletion polymorphisms (INDELs). A total of 189 unrelated Aymaras from Puno and 172 unrelated mestizos from Peru were genotyped for the 46 INDELs in a single PCR multiplex, and compared with data from 273 African, 346 European and 64 Native American individuals. According to the results obtained, the proportion of Native American ancestry predominates in the Aymara population (90.7%), followed by 8.0% European and 1.3% African ancestry. As expected, the Native American ancestry was lower in the Mestizo population sample (69.5%) than in the Aymara, with higher proportions of European (26.4%) and African (4.1%) admixture.