By traditional classification, there are five Cyclotus taivanus subspecies in the low mountainous area of Taiwan and Okinawa: C. taivanus adamsi, C. t. dilatus, C. t. diminutus, C. t. peraffinis, and C. t. taivanus. The molecular phylogenetic relationships of this group have never been discussed. In order to investigate the relationships between C. taivanus ssp., we sequenced part of the mitochondrial COI and the 16S rRNA gene from 26 sampling sites. We also measured 9 shell traits for morphological analysis. Even though morphological PCA analysis revealed a more or less continuous distribution of individuals in morph-space, the two highly divergent haplotype clades in molecular analysis indicated the presence of two independently evolving lineages. Our results indicated that the sequence divergence between the two independent clades was almost as high as that among other Cyclophoridae species found previously. Therefore, from the viewpoint of taxonomy, C. t. adamsi should be considered a valid species, and we here raise the current taxon to a full species: C. adamsi. By environmental analysis, temperature was found to be a limiting factor in the distribution of C. adamsi and the C. taivanus group (C. t. dilatus, C. t. diminutus, C. t. peraffinis, and C. t. taivanus). The ecological divergence is probably a rule of speciation in our case. The PLS (Partial least square) analysis results indicate that phenotypic plasticity may be a key element of the variable shell in the C. taivanus group. The speciation process is not complete among the C. taivanus group, and the adaptation to climatic pressure continues to be a rule of the speciation process.