Abstract: This paper deals with the sequence analysis of mitochondrial 12S rRNA gene fragment and phylogenetic relationship of three mud crabs , Scylla serrata (Forsk l) , S . oceanica (Dana) and S. tranquebarica (Fabricius) collected from Japan , Thailand and . Madagascar. The result indicated that there was length variation among three mud crabs , which was 422bp , 426 bp and 425 bp respectively. Genetic distance inter2species was greater than that intra2species. Trees constructed by distance method and maximum parsimony method using Charybdis japonica and Thalamita prymna as the outgroup indicated that there were three distinct clades corresponding to S . serrata , S . oceanica and S . tranquebarica respectively. It suggested that the three mud crabs should be recognized as valid species and managed as different fishery management unit.