Mud crab is high-value species and become importance aquaculture species in coastal provinces in Vietnam. Annually, approximate 100 million of juvenile crabs are produced from over 150 hatcheries. Although mud crab has been cultivated in Vietnam a long time but researches about taxonomy of mud crab are limited because of mainly basing on morphometric. This study present results of identifying mud crab species using mitochondrial DNA sequencing. Thirty three mud crab samples collected from 10 provinces in Vietnam, Australia were sequenced in COI region. The Vietnam mud crab sequencing also were compared with DNA sequences of mud crab in China, Australia and Indonesia. Results showed COI region is useful for mud crab identification. Four mud crab species was found in Vietnam: Scylla paramamosian, S. serrata, S. olivacea and S. tranquebaria in which S. paramamosian is the most popular. Phylogenetic supports the S. paramamosian closer relationship S. serrata and S. tranquebaria than S. olivacea species. These results have made the remarkable contribution to developing taxonomy systems as well as selecting materials for selective breeding programs and conservation of these species in Vietnam.