Aim We investigate the biogeographical history of the species‐rich Sundaic freshwater crab genus Parathelphusa (family Gecarcinucidae). In particular, we ask to what extent eustatic sea‐level fluctuations influenced diversification and species distribution. We test the prediction that sea‐level fluctuations in the course of the Pleistocene glaciations increased speciation rates. Location Malay Peninsula, Greater Sunda Islands (Borneo, Java, Sumatra, Sulawesi), Bali and the Philippines (Palawan, Mindoro). Methods Phylogenetic inference calculations were based on partial mitochondrial cytochrome c oxidase subunit I (COX1), 16S ribosomal RNA and nuclear histone subunit 3 (H3) genes using maximum likelihood, maximum parsimony and Bayesian approaches. Divergence time estimation was performed with beast based on external substitution rates. Biogeographical analyses were conducted with a parametric likelihood method (Lagrange) and a Bayesian method (BayesTraits). Lineage diversification was studied with a lineage‐through‐time plot, and a maximum likelihood approach as implemented in the R package laser. Results We propose a Late Miocene age for the most recent common ancestor of Parathelphusa, with an ancestral range covering Borneo and the adjacent part of Sundaland. The evolution of six lineages pre‐dates the Pliocene, five of them occurring on Borneo. Subsequent dispersal during the Miocene and Pliocene extended the range of Parathelphusa to the Philippines, Sulawesi, the Malay Peninsula and Sumatra, and, during the Late Pliocene and Pleistocene, to Java. Pleistocene divergence occurred between species from the Malay Peninsula and Sumatra, Java and Sumatra, and Java and Borneo. Main conclusions Although low sea levels during the Pleistocene in all probability facilitated the dispersal of freshwater crabs among the Greater Sunda islands (excluding Sulawesi, which is not part of the Sunda Shelf), there is no complete Pleistocene geographical admixture of species, and pre‐Pleistocene biogeographical patterns were retained. Furthermore, Pleistocene vicariance did not lead to an increased diversification rate in Parathelphusa. Instead, single colonization events out of Borneo during the Neogene, followed by species radiation (e.g. on Palawan and Sulawesi), contributed substantially to species diversity in Parathelphusa. This involved the crossing of marine barriers such as the Wallace Line.