Phylogenetic relationships of the genus Cuora sensu lato (Cuora sensu stricto and Cistoclemmys) and other testudinoid genera were inferred from variations in 882 base positions of mitochondrial 12S and 16S rRNA genes. Results yielded a robust support to the monophyly of a group (Cuora group) consisting of Cuora sensu lato and the monotypic Pyxidea. Within the Cuora group, the continental Cuora (sensu stricto) and the two subspecies of Ci. flavomarginata constituted two well-supported monophyletic groups. Distinctly small interspecific genetic distances in the former groups suggested that in the continent speciations in Cuora took place much later than the primary divergences in the Cuora group, or speciations in other related genera, such as Mauremys. Our analyses failed to provide a substantial support to the monophyly of any other combinations of taxa within the Cuora group, including Cuora in broad and strict senses, and Cistoclemmys as consisting of Ci. galbinifrons and Ci. flavomarginata. Besides these, our results also suggested the non-monophyly for the Batagurinae and the Geoemydinae, and sister relationships of the Bataguridae with Testudinidae rather than with the Emydidae.