Alternative models of residential mobility have been proposed to explain the development and spread of Tiwanaku influence across the south central Andes. Within the Osmore drainage, the rich Moquegua Valley has been hypothesized as the site of a significant colonization event (or events) whereby both the natural and human landscape was transformed and integrated into the expansive Tiwanaku state. In this research, the impact of altiplano colonization is inferred from temporal and spatial patterns of genetic variation within and among native groups. Mitochondrial DNA haplogroup frequencies are used as the measure of genetic variation. The haplogroup data are determined for Moquegua Valley archaeological samples (Chen Chen site; A.D. 785-1000) and are compared to published data from 58 other ancient and contemporary native groups. The results support temporal and spatial genetic continuity in the south central Andes for the last 1,000 years. Contemporary Aymara speaking groups are exceptions to this pattern, perhaps because of recent population decline. While the altiplano colonization hypothesis is not rejected, moderate gene flow and relatively large population sizes likely characterized much of south central Andean prehistory regardless of the contribution from Tiwanaku colonization events.