Abstract: The mitochondrial DNA COI genes of 17 individuals from three populations of Macrobrachium rosenbergii (F1 of Burma wild population, Jiangsu cultured population and F2 of Guangxi breeding population) were amplified by PCR method and totally sequenced。498bp long of partial nucleotide sequences were aquired and applied to study the genetic diversity difference among this three populations。The analytical results indicated that in the COI gene locus, F1 of Burma wild population had relatively abundant genetic polymorphism,while polymorphism of Jiangsu cultured population and Guangxi breeding population were very poor。10 polymorphic sites and 5 haplotypes were found in the sequences of 17 individuals。The average nucleotide divergences in three populations respectively were 0.88%，0.07% and 0,The UPGMA phylogenetic tree suggested that F2 of Guangxi breeding population and Jiangsu cultured population had a closer genetic relationship,their individuals gathered together to be a genetic branch；F1 of Burma wild population diverged to be another relatively independent branch。 For the distinct nucleitide differences, COI gene was suitable as a genetic marker to distinguish this two branch of Macrobrachium rosenbergii population。