The phylogenetic relationship of the two grapsid crabs Selatium brockii and Nanosesarma minutum collected from mangrove creeks have been studied corresponding to the mitochondrial genome cytochrome oxidase subunit I (COI) gene. Genomic DNA was isolated from the claw muscle of the two crabs Selatium brockii and Nanosesarma minutum. The COI gene of the crabs was amplified and sequenced. The phylogenetic tree was constructed from the COI gene sequence. Present findings show that the genetic relationship between these two species to be 74% and both the species show 99% similarity to Parasesarma erythrodactyla strain MSCAS9 (KX018517), a red handed shore crab found in the mangrove creeks. COI gene could be a useful molecular marker to determine the monophyly of a crustacean family. No earlier reports were available on the molecular phylogeny of currently studied species. Increase in the taxon sampling of COI gene sequences from different groups could be a promising methodological resolution for determining the genetic divergence of the species.