Known-locality samples of Geoemyda spengleri from three Chinese provinces (Guangdong, Guangxi, Hainan) and northern Vietnam provide clear evidence for phylogeographic structure in a southern Chinese chelonian species. Within southern China two clades of mitochondrial haplotypes from east and west of the Xi Jiang together form the sister group to haplotypes from northern Vietnam. Turtles from Hainan Island harbour haplotypes of the same clade as turtles from Guangxi, 400 km distant. These findings suggest that phylogeographic differentiation may have once existed in other co-distributed, highly endangered chelonian species. The possibility of phylogeographic structure should be considered in any in-situ and ex-situ conservation program for Chinese chelonians.