Mitochondrial CR gene and COⅠ gene fragments were amplified and sequenced from 9 wild stocks of Portunus trituberculatus in China.Respectively,530 bp and 584 bp long partial gene fragments of the CR gene and the COⅠ gene were obtained.A+T mean contents of the CR sequences and the COⅠ sequences were respectively 73.2% and 62.2%.Moreover,66 haplotypes were identified from 83 samples with 91 variation sites of CR gene and 33 haplotypes were identified from 96 samples with 42 variation sites of COⅠ gene.The genetic distance and cluster analysis showed that genetic distances were nearest among six stocks of Yellow Sea,East China Sea,Bohai Sea,while the genetic distances were nearest among three stocks of South China Sea.The fixation indices (F st) were from -0.074 54 to 0.270 87 between any two stocks and some of them got to significant and great significant level.So these indicated that there were some genetic differentiations in different wild stocks of P.trituberculatus in China.