There are 5 freshwater crab species of the genus Geothelphusa Stimpson, 1858 (Crustacea: Brachyura: Potamidae) in southernmost Taiwan, G. albogilva Shy, Ng and Yu, 1994; G. ferruginea Shy, Ng and Yu, 1994; G. tawu Shy, Ng and Yu, 1994; G. lanyu Shy, Ng and Yu, 1994; and G. lutao Shy, Ng and Yu, 1994. Among these, G. lanyu and G. lutao, are only known from 2 offshore islands, Lanyu (Orchid I.) and Lyudao (Green I.), respectively. Comparisons of the DNA sequences encoding part of the mitochondrial large subunit 16S rRNA gene showed that all 5 species constitute a single monophyletic clade distinct from species in nearby areas. The genetic and morphological differences among G. tawu, G. lanyu, and G. lutao are very small, and further studies may show that all 3 are conspecific. This is supported by the geological history of the area, with both islands having a violent volcanic history, and the presence of freshwater crabs on the island must have been a relatively recent event (~500,000 years), and may even have been the result of human introduction. The phylogeographical patterns of the genus in southernmost Taiwan and adjacent areas were examined at the molecular level, and the isolating effects of mountains on freshwater crab dispersal are discussed. The genetic data also suggest that the 2 species from southwestern Taiwan, G. pingtung Tan and Liu, 1998 and G. neipu Chen, Jeng and Shy, 1998, are synonymous, with the former name having priority.