Cryptic lineages present major challenges for evolutionary and conservation studies, particularly where these lineages remain undiscovered. Freshwater crabs are known to harbour cryptic diversity, in most cases with limited morphological differences. During the present study, we used a multilocus (12S rRNA, 16S rRNA, COI, 28S rRNA, DecapANT and PEPCK) Bayesian species delimitation to examine cryptic diversity within a freshwater crab species complex (Potamonautes clarus/P. depressus). We sampled 25 highland rivers in the Tugela and uMkomazi River drainage systems of the Drakensberg Mountain range, in the KwaZulu–Natal province of South Africa. Our results showed there to be at least eight lineages: six novel potamonautid freshwater crabs, and two described taxa P. clarus and P. depressus. Divergence from the most recent common ancestor occurred between the mid- and late Miocene (12.1 Mya), while divergence within the species complex occurred ∼10.3 Mya up until the Holocene (0.11 Mya). The discovery of six novel lineages of freshwater crabs from a seemingly restricted distribution range has conservation implications, but to date most conservation planning strategies have focussed on freshwater vertebrates. By conducting a fine-scale phylogenetic survey using invertebrates, this study provides a platform for the inclusion of freshwater invertebrates in future conservation assessments.