Ancestry Informative Markers InDels (AIM-InDels) show high allele frequency variation between ancestral populations and are useful to estimate individual and population ancestry. This work determined the African, European and Native American admixture proportions in a population sample of 126 individuals from Tunja, Department of Boyaca, Colombia. This region is located close to the center of the country and has a diverse population. To estimate the African, European and Native American admixture proportions, in the sample there were used as parental populations, the genetic profiles of 319 individuals (Africans: 105, Europeans: 154, and Native Americans: 60). The ancestry analysis of this population revealed a main European contribution (55%) with an important contribution of Native American ancestry (40.8%) and only 4.2% contribution of African descent. The results obtained from this type of studies allow us to have a real approximation of the state of the different Colombian populations, after a history of colonialism and years of war with high levels of displacement of the civilian population.