Achalinus niger is an endemic species of Taiwan. It distributes from 1000 to 3000 m in altitude. The effect of geological isolation, especially mountains and valleys may influence the population genetic structure of the species. The ND2 gene was used as genetic marker to analyze the genetic structure of populations and phylogeography of A. niger. The mean genetic distance is 3.87¢H and the mean nucleotide diversity 3.5¢H. The Meifeng population was distinct in genetic structure from other populations. The data suggest that A. niger had more than one incursion events. In phylogenetic analyses, there were three major lineages in A. niger, and these lineages were correlated to geographic distribution. Lineage¢¹ was sampled from northern Taiwan, lineage¢º from southern Taiwan, while lineage ¢» from Meifeng only. The result of AMOVA indicated that there were high genetic variations among groups. The genetic isolation and geographic distribution of these groups probably resulted from the geographic barriers.