Abstract: MtDNA cytochrome b gene sequence variations of samples of two bagrid fishes from Changjiang and Zhujiang Rivers were studied in the present paper. 1137 bp sequences were obtained through PCR amplifications.Sequence analysis was conducted using MEGA program with the sequence of the common carp downloaded from GenBank for comparison.The results showed that there is a codon deletion in cytochrome b gene of the two bagrid species at the tenth nucleotide position compared with that of the common carp, which could be a common character for all catfishes. The intraspecific sequence divergences of Pelteobagrus fulvidraco and Mystus macropterus were 0.4% and 1.6% respectively,which were in the range of freshwater fishes,but higher than those of anadromous fishes.The sequence differences between P. fulvidraco and M. macropterus were from 17.6% to 18.0%, which were much higher than the intraspecific variations. Inferred from the molecular evolution rate,the divergent time of M. macropterus in Changjiang and Zhujiang rivers was about 270 thousand years ago during middle and late Pleistocene,and that of P.fulvidraco was 70 thousand years ago in the late Pleistocene.The reason that the two bagrid fishes in Changjiang and Zhujiang Rivers have different divergent times might be that M. macropterus is warm fresh water fishes,and they were limited to the south of Changjiang River in China during the middle and late Pleistocene glacial period and differentiated in different water systems till now; while P.fulvidraco is a widespread species and can adapt to different environments, thus exchanges among P.fulvidraco populations might have occurred among different water systems during the Quaternary glacial period.