The genus Omalonyx d'Orbigny, 1837, includes neotropical semi‐aquatic succineid slugs and comprises six recognized species to date. Field surveys across continental South America recovered five of the six recognized species. According to the morphological characters traditionally included in Omalonyx descriptions, the specimens were tentatively identified as O. matheroni, O. pattersonae, O. convexus, O. geayi and O. unguis. Employing sequences of mitochondrial cytochrome oxidase I (COI) alone or combined with the nuclear second internal transcribed spacer (ITS2) in discovery methods of species delimitation (GMYC and STACEY) led to species delimitation hypotheses that, except for unambiguously supporting O. convexus, have no correspondence to morphologically based assignments. To choose the delimitation model that best fit our data, the hypotheses recovered by GMYC, STACEY and morphology and created by merging species recovered by those methods had their marginal likelihood estimated and compared using the Bayes factors. The best‐supported hypothesis distinguished two species besides O. convexus: one widespread over most of South America and the other restricted to Rio de Janeiro State, Brazil. Furthermore, the pattern of genetic structuring supports pathways connecting the Amazonian and Atlantic forests. This pattern is similar to that observed in terrestrial taxa (e.g., forest‐dwelling small mammals) and is different from the pattern for fully aquatic taxa.