Fish are important for food supply, especially in developing countries. In Southeast Asia, including Myanmar, the mud crab fishery is an important livelihood that represents a valuable source of income and food to coastal communities. However, the increasing demand for mud crab in domestic and international markets and poor management has generated concern about the status of this fishery across Southeast Asia. In this region, at least four species of mud crab in the genus Scylla are recognised but their correct identification and occurrence remain to be fully explained. Relying on accurate taxonomic identification of mud crab species represents the cornerstone of the successful implementation of management plans as life history biology and relative exploitation rates may vary by species due to gear susceptibility. Toward this aim, tissue samples from mud crabs were collected from four fishing communities of the Mergui archipelago, in the Tanintharyi region of southern Myanmar. All crab samples were DNA barcoded for species identification through sequencing. This study is the first genetic characterization of the mud crab fishery in Myanmar and revealed that Scylla olivacea was the only species found in the sampled fisheries of the Tanintharyi region. The populations studied across the Mergui archipelago did not show evidence of genetic structure, but gene flow appeared to be limited among conspecifics from neighbouring countries.