Crabs from the Mithrax–Mithraculus species complex are known for their diversity of lifestyles, habitats, and coloration. This group includes small, colourful, symbiotic species and much larger, reef-dwelling crabs targeted by fishermen. The evolutionary relationships between the species within this complex are not well-defined. Previous studies based upon morphological characters have proposed the separation of this complex into two genera (Mithrax and Mithraculus), but cladistic analyses based upon larval characters do not support this division. A molecular phylogeny of the group may help to resolve this long-standing taxonomic question and shed light on the ecological conditions driving the diversity of these crabs. Using a 550-bp alignment of the 16S rRNA mitochondrial DNA segment we examined the phylogenetic relationships between 8 species within the Mithrax–Mithraculus complex native to the Caribbean. The resulting phylogeny indicates that this complex is paraphyletic, as it includes the genus Microphrys. The analyses revealed a well-supported, monophyletic group containing four species of Mithraculus (M. cinctimanus, M. coryphe, M. sculptus and M. forceps) and supported one pair of sister species from the genus Mithrax (M. caribbaeus and M. spinosissimus). No complete segregation of species, according to genera, was evident, however, from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of alternative trees in which monophyly of the two genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the genera Mithrax and Mithraculus. A review of the literature demonstrated considerable phenotypic variation within monophyletic clades in this group.