Objectives. To review the Two-Layer Hypothesis for modern humans’ population history of East Asia. According to the most recent version of this hypothesis, the first layer stemmed from the late Pleistocene colonization of the region from China to Australia/Melanesia, and the second layer stemmed from an independent, late Pleistocene colonization of Siberia. During the Holocene, second-layer populations with an agricultural subsistence expanded southward into China and Southeast Asia. Materials and Methods. The materials are samples from Sri Lanka throughout East Asia to Australia/Melanesia and the Americas. These have been comparatively analyzed by Hirofumi Matsumura for their cranial metric and dental metric shape, and dental anatomical traits. The methods involve assigning each sample in each analysis to one of the two layers recognized by Matsumura. Results. Overall, Matsumura’s two layers are distinct from each other. However, there are some samples with consistent affinities to the layer other than that to which they are correctly assigned, and some samples with indeterminate affinities to either layer. Discussion. The available evidence suggests that the cranial metrical shape of the second layer evolved from an ancestral first layer cranial metrical shape, both in Mainland Southeast Asia and in Northeast Asia. However, Holocene population expansion within Mainland Southeast Asia was limited whereas, in keeping with the Two-Layer Hypothesis, population expansion from Northeast Asia southward during the late Holocene was major and widescale. That said, some Southeast Asians with an agricultural subsistence have retained a first-layer cranial shape until as recently as the present.