We sequenced and analyzed partial nucleotide sequences of Cyt b and COⅠgene for Nemipterus species,including Nemipterus virgatus, N. japonicus, N. bathybius, N. nemurus, N. mesoprion, and the COⅠgene of N.hexodon, N. peronii and N. furcosus from GenBank. The results show that there are little different in nucleotide base of Cyt b (425 bp) and COⅠ (507 bp) . The divergence of sequences and genetic distances are tiny in N. japonicus and N. nemurus (COⅠ0.25% and 0.003, Cyt b 0 and 0) which suggest they have very closed relationship. And the Nemipterus species belongs to one genus, including N.peronii since the N. japonicus and N.mesoprion are in different branches. From the NJ phylogenetic trees, N. japonicus and N. nemurus are the latest differentiation species, N. virgatus is the oldest one . Molecular evolution rate (2% every million year in Cyt b ) showed the divergence of Nemipterus species occurred during the middle pleistocene epoch. It is a reference of the classification of Nemipterus species.