This study focuses on the cranio-morphometric analysis of female skulls from several prehistoric hunter-gatherer sites; Yahuai Cave in Guangxi (ca. 16,000 BP), Bau Du in Vietnam, and Xiaoma Taiwan (ca. 6000–5300 BP). The aim of this research is to test the “two-layer model” of human dispersal in Southeast Asia. The resulting craniometric data indicated that the examined specimens all belonged to the “first layer” of dispersal and shared a common ancestry with contemporary Australo-Melanesians. These individuals all pre-dated the expansion of agricultural colonizers of East/Northeast Asian origin—that is, the “second layer” of dispersal. Additionally, global scale comparisons reveal that the peoples of the ‘first layer’ colonization of Southeast Asia are morphometrically close to Africans, suggesting that early hunter-gatherers examined in this study were direct descendants of anatomically modern humans who migrated from Africa.