The freshwater crabs Geothelphusa tawu, G. lutao and G. lanyu from southern Taiwan and the offshore islets, Lyudao (= Green I.) and Lanyu (= Orchid I.) are closely related in morphology and genetics, and have been proposed to be the same species. Examination of a series of specimens collected from the distributional ranges of the three species indicated that key characters of the ambulatory legs and the male first gonopod are too variable to support the identity of three species. Based on the mitochondrial 16S rDNA and COI sequences, the phylogenetic analysis did not recover three clades corresponding to the three species, but only a main clade without further clear grouping. The interspecific distances of nucleotides are also too small to support the species delimitation. We conclude that the three species should be treated as a single species. Additionally, unique haplotypes of COI have been found in Lyudao and Lanyu, which are hypothesized as two founder populations that colonized the islets from the Taiwan main island during glacial maxima.