In order to investigate the genetic diversity among three populations of Macrobrachium rosenbergii collected from Shanghai breeding population (SC), Zhejiang cultured population (ZJ) and Thailand wild population (TL), the mitochondrial sequences of the COⅠ gene in the three populations were amplified and determined by PCR and sequencing. The result showed that 8 nucleotide sites and 4 haplotypes were found in the 458 bp long partial gene segment. The mean content of A+T (54.4%) was higher than G+C (45.7%). Genetic variation parameters showed the population of highest haplotype diversity was TL population (Hd=0.733), the population of highest nucleotide diversity was ZJ population (π=0.005). AMOVA showed that genetic variations among populations (74.5%) was higher than that within populations (25.5%). The tendency of molecular phylogenetic trees which were constructed by NJ and UPMGA method was similar. SC population and ZJ population were the closest genetically, and they clustered into a small branch, then with TL population. These findings were expected to provide reference information for the protection and utilization of germplasm resources of M.rosenbergii.