The primers of Eriocheir sinensis and Eriocheir japonica were designed by using the sequences of mitochondrial DNA 12S rRNA region of Drosophila yakuba and Daphnia pulex . 457 base pairs of encoded 12S rRNA region of mitochondrial DNA were amplified and sequenced. The length of sequence of two species was the same, the A, T, G, C content s were similar, which were 159bp( 34. 79%) , 177bp( 38. 73%) , 51bp( 11. 16% ) , 70bp ( 15. 32% ) and 159bp ( 34. 79%) , 178bp ( 38. 95%) , 50bp ( 10. 94% ) , 70bp ( 15. 32% ) respectively. Between E. sinensis and E . japonica , there were 5 different sites, that were transition sites at 98bp, 151bp, 317bp, 417bp, and transversion site at 294bp.