The results of an analysis of cranial measurements obtained from 223 skeletal samples, exhumed in 11 archaeological sites of Arica littoral and the Azapa valley, in extreme north Chile are presented. The object of this analysis is to reconstruct the biological history of the prehistoric inhabitants of the coast and the valley, in the context of their interaction with demographically and culturally more developed centers around Lake Titicaca. To this end, an osteological collection exhumed in that region is included in the analysis. The results reveal the microevolution of a coastal population with Andean roots that possibly arrived at the coast of Arica some 9,000 years ago, whose phenotypic features are recognizable until the time of contact with populations of the XVI century. This group gave origin to the inhabitants of the valleys, which during the Formative Period (3,500 B. P.) became farmers. The coastal groups maintained contact with certain groups from the valley (AZ-70). Nevertheless, the characteristic coastal features are accentuated starting from the Late Archaic Period (PLM-7 site), possibly due to genetic drift not compensated for by immigration. During the Formative Period, gene flow occurred from the highlands to the valleys, judging by a decrease in biological distance. This flow reached its maximum intensity in the Middle Horizon and the Late Intermediate Period (AZ-8). It is suggested that the migrations from the highland to the valleys are related to the disintegration of Tiwanaku.