The Indo-Pacific genus Metopograpsus belongs to the family Grapsidae and comprises six species of intertidal crabs inhabiting sheltered rocky shores and mangrove forests. All species are opportunistic feeders and four of them are associated with roots and trunks of mangroves. So far, no comprehensive molecular phylogenetic study has been conducted on this genus, despite the fact that some species are not easily separable from a morphological point of view. We performed a phylogenetic and phylogeographic investigation based on sequences corresponding to both ribosomal mitochondrial DNA genes from 44 samples of Metopograpsus spp., covering the distribution ranges of each species. Our main aims were to validate species identification across their respective distribution ranges and depict the phylogeographic patterns within each species. Our phylogenetic inference reconstructions confirmed monophyly of the six species. We also recorded a high intraspecific genetic variation and strong phylogeographic structure within M. thukuhar and M. quadridentatus. This indicates the occurrence of distinct evolutionarily significant units within these two taxa, possibly corresponding to undescribed species. Further nuclear DNA-based phylogeographic analyses, as well as morphological investigations, will be necessary to assign a taxonomic value to the recorded evolutionarily significant units.