In epidemiological studies, it is easier to glean information from isolated populations with simple genetic backgrounds than from populations with relatively complex genetic backgrounds. Regarded as an isolated population, the Minz (Hei-Yi Zhuang) in Napo County (in the China-Vietnam borderland) has been the subject of numerous recent studies. To assess the genetic isolation of this population, we studied Y chromosome and mitochondrial DNA from Minz and Han in Napo. Both populations exhibited southern Chinese genetic characteristics in both paternal and maternal lineages. Using NETWORK analyses, we found pronounced gene flow between these two populations only in maternal lineages. We also observed gene flow from other populations into the Minz gene pool. We thus concluded that the Minz is not a genetically isolated population and it is increasingly difficult to find isolated populations in mainland East Asia.