Aim: Based on mitochondrial DNA (mtDNA) data, many organisms with ranges spanning multiple biogeographical regions exhibit genetic structure across the transition zones between these regions, while others appear to be genetically homogenous. No clear link has been found between the presence or absence of such spatial genetic discontinuities and species' dispersal potential, confounding the formulation of general predictions concerning genetic structure. The fact that discrepancies between mtDNA and nuclear markers are common across semi-permeable barriers suggests that a lack of structure could be attributable to mtDNA-specific properties of inheritance. We re-examined genetic structure in the coastal crab Hymenosoma orbiculare, a species that is represented by a single mtDNA lineage across the Atlantic/Indian Ocean biogeographical transition zone, by comparing mtDNA data with nuclear DNA data. Location: South Africa's cool-temperate and warm-temperate marine biogeographical provinces. Methods: DNA sequence data from the mitochondrial COI gene and the intron of the nuclear ANT gene were generated for 150 individuals of H. orbiculare. For each locus, we determined whether the sharing of alleles between provinces was the result of either the retention of ancestral polymorphism or of secondary contact. Results: We recovered two nuclear intron lineages whose spatial genetic structure reflects contemporary biogeographical and oceanographical conditions, indicating that the existence of a single mtDNA lineage is not a function of unexpectedly high levels of dispersal. Main conclusions: MtDNA-based genetic homogeneity is increasingly being reported in coastal organisms with ranges spanning biogeographical transition zones that define distinct evolutionary lineages in other species. Our results stress the importance of revisiting single-locus data sets by means of multilocus genetic approaches before any conclusions can be drawn about the role of biogeographical transition zones in driving genetic structure.