A higher density of evidence in terms of both temporal and geographical variation is needed for the understanding of the population history of East/Southeast Asia. We report here two skulls of the hanging coffin people from the ancient Tang dynasty of Yunnan province, China, and compare them with other Neolithic to modern human groups of East/Southeast Asia. The cranial series of the hanging coffin people can be regarded as a single population distinctive among the comparative samples. They share a low and wide face but exhibit variation in nasal root protrusion and alveolar prognathism. Evaluation of biological affinities based on multivariate craniometry indicates that the hanging coffin people are unique, being distant from modern mainland Asian groups and rather close to the Neolithic Zhenpiyan of south China. The peripheral position of the hanging coffin people relative to the mainland Asian groups appears to parallel the situation seen with modern Andaman islanders, or aboriginal Australians. This is interpreted as indicating the influence of a bottleneck effect in a locally isolated population within a more global trend of population history of East/Southeast Asian.