A study of the Inka origins and their lineages was performed in twelve contemporary families with presumed patrilineal lineage to Inka monarchs. A comparison of Y-chromosome and mtDNA markers of these descendants with a database of about 2400 South American native individuals of Peru, Bolivia, Brasil and Ecuador showed two distinct patrilineal clusters, and a very diverse matrilineal origin. In addition they show great affinity to areas South of Cusco including the Lake Titicaca.