The influence of tropical lowland migrations on the emergence of cultural change in the Central Andes has been postulated in general terms since the beginning of last century (Tello 1929). Archeological and molecular genetic evidence, particularly agriculture of tropical cultigens and ancient mtDNA haplogroup typing in northern Chile, suggest a chronologically more precise relationship between both regions. We test in this article the hypothesis that the process of cultural transformation of prehistoric populations living on the coast and the desert valleys of northern Chile can be partially linked to gene flow from the eastern slopes of the Andes and/or from the tropical lowlands during the Late Archaic / Formative periods (ca. 3,500-2,000 B.P.).