Species of Pelteobagrus nitidus and Pelteobagrus eupogon are endemic to East Asia, which are the specimens in the present study. MtDNA ND4 (plus three 3' flanking tRNAs: histidine tRNA, scrine tRNA and partial leucme tRNA) gene sequence variations of these two species from different drainages were studied in the present study. About 772 base pair sequences were obtained through PCR amplification. Sequence analysis was conducted using MEGA2. I software. Hemibagrus macropterus was selected as out-group. The Kimura's 2-parameter distances were calculated. The genetic distances among P. nitidus were from 0.000 to 0.012, and the genetic distances among P. eupogon were from 0.000 to 0.003. The genetic distances between P. nitidus from different drainages and P. eupogon were from 0.099 to 0.108, which suggest that P. nitidus and P. eupogon are two valid species. The genetic distances among P. nitidus from different drainages were small, the same as P. nitidus in the same drainages. The possible reasons are the following: (i) there are frequent gene flow among P. nitidus samples from different drainages;( ii) the evolution rate of the East Asian bagrid mitochondrial DNA is relatively slow;( iii) the human economic activities have probably caused change of genetic population structure of P. nitidus.