The basic information on genetic diversity and population structure is essential for the construction of appropriate management schemes leading to sustainable fisheries of the blue swimming crab (Portunus pelagicus). Here, genetic heterogeneity of P. pelagicus (N=174) was examined by single-strand conformational polymorphism (SSCP) analysis of mitochondrial cytochrome c oxidase subunit I (PpCOI270). Seven SSCP genotypes were found across all investigated samples. The average genetic distance between pairs of geographic samples was 0.0014-0.7247. Significant geographic heterogeneity (P0.05; 6.54 and 16.17 individuals per generation) located in the same coastal regions. Therefore, the gene pool of P. pelagicus in Thai waters was genetically differentiated to different stocks even though it is biologically regarded as a potential dispersal species. Five geographic samples of P. pelagicus in Thai waters could be differentiated to three genetic stocks; Chanthaburi and Suratthani (stock A), Prachuap Khiri Khan (stock B) and Ranong and Krabi (stock C).