The soil animal Mongoloniscus sinensis (Dollfus, 1901) is distributed in Northern China together with three other congeneric species only found in Asia. Compared to European and North American Oniscidea, little phylogeographic information about this Asian genus has been reported. Herein, we infer the genetic structure and demographic history of M. sinensis based on mitochondrial cytochrome c oxidase subunit I (mtCoI). The total dataset included 193 individuals from 26 locations in four provinces (Shanxi, Henan, Hebei and Shandong) of China. Most of the 87 haplotypes were unique to a sampling location, but seven haplotypes were shared among the populations. The results showed that high genetic differentiation exists both within populations and among the groups and populations of M. sinensis. According to the distribution of phylogenic clades and geographic analyses, it is suggested that mountain ranges play an important role in population separation and that the possible evolutionary trajectory of this species is from north to south. The most likely place of origin is the Northeast Plain of China with an estimated time of isolation separating populations around 8 Mya.