The structure of the male gonopods of millipedes has been considered to be species-specific. As such, gonopods—which aid in copulation and sperm transfer—are used in the taxonomic diagnosis and description of species. However, it was recently demonstrated that gonopod morphology is not always characteristic of species. Diagnoses based on gonopod morphology can therefore result in underestimation of taxonomic diversity amongst millipedes. On the basis of this observation, we examined genetic variation in two populations (approximately 250 km apart) of a widely distributed and colour-polymorphic southern African millipede, namely Bicoxidens flavicollis Attems, 1928. An analysis of genetic divergence based on 520 nucleotides of the mitochondrial cytochrome oxidase 1 gene, and 684 nucleotides of the mitochondrial 16S rRNA gene, demonstrated high levels of divergence (19.09% for cytochrome oxidase 1 and 6.66% for 16S rRNA) between the two populations. These results suggest the presence of cryptic species in B. flavicollis and, furthermore, corroborate observations that taxonomy based on gonopod morphology may be too inclusive.