In order to clarify whether the populations of Pelodiscus from the main islands of Japan are indigenous or artificially introduced, we constructed a mitochondrial phylogeny among samples from Japan and adjacent regions. The results strongly suggested the presence in Japan of various mitochondrial haplotypes that largely formed two divergent groups, one supposedly corresponding to P. sinensis (Wiegmann, 1834) sensu stricto and the other to P. maackii (Brandt, 1857). Haplotypes putatively associated with P maackii were unique to, and broadly prevailing in Japan. This may reflect indigenous nature of P. maackii in Japan, which would be more appropriately referred to as P. japonicus (Temminck and Schlegel, 1835). The others, putatively associated with P. sinensis, were fewer in Japan, and included those shared with individuals sold in a fish market of the continental China, suggesting the current Japanese P. sinensis to be exotic.