The chiton genus Cryptoplax is widely distributed in the Indo-Pacific, extending to southern Australia and the northwestern Pacific (NWP), with 17 recognized species. Among these species, Cryptoplax japonica is commonly found on rocky intertidal and subtidal substrates in the NWP, whereas another species, C. propior, is rarely seen because of its cryptic subtidal habitat and limited distribution. In this study, we surveyed the genetic diversity of C. japonica populations based on 93 individuals from 24 sampling sites along the Korean and Japanese coastlines, including the type locality, using DNA sequences of the mitochondrial gene cytochrome c oxidase subunit I (COI). Haplotype network and phylogenetic analyses of COI sequences revealed two highly divergent genetic lineages of C. japonica separated by a large pairwise genetic distance (10.62%), which was comparable to the genetic difference when either of these two lineages (A or B) is compared with the co-occurring C. propior. In addition to COI sequences, average sequence divergence in 16S rDNA between these three lineages ranged from 2.0 to 3.3%. In contrast to this deep sequence divergence, both morphological examination of radula, girdle and articulamentum colouring, and morphometric analyses of shell measurements using principal component analysis and linear discriminant analysis revealed no diagnostic differences between the two C. japonica lineages. The co-occurrence of these two divergent lineages within most of our studied area, with no morphological differences, indicates cryptic divergence. More extensive sampling from the entire distributional ranges of these cryptic species, in combination with the use of additional molecular markers could shed light on the mechanisms underlying their divergence.