The ground inhabitant camaenid land snail Satsuma nux is an endemic species to Taiwan and widely distributed throughout the western region. In this study, we applied partial mtDNA CO 1 gene sequences to survey the genetic structure from eleven localities and sixty-eight individuals were analyzed from these different localities. The population genetic structure was shown to diverge into three subclades with different genetic characteristics and no apparent gene flow in-between. The southern population exhibits the highest genetic diversity; in contrast, the northern population from Hsinchu has a lower genetic variation. Furthermore, the northern population was analyzed and shown to have a considerable genetic distance from the others. Samples akin to S. nux collected from Kaohsiung, Hualien, Taitung and Pingtung were analyzed to give significant genetic variation and placed on a different clade in the phylogenetic tree, thus infer belonged to a different taxa on the species level.