The mtDNA cyt b gene of yellow catfish from five lakes in the middle and lower reaches of the Yangtze River was amplified and sequenced.Result showed that the average contents of A+T were a little higher than that of G+C in the aligned sequences of 955 bp.54 variable sites were detected and 37 haplotypes were recovered.The haplotype diversity and nucleotide diversity were 0.945±0.018 and 0.00419±0.00043,respectively.The genetic distance between Lake Taihu population and Lake Gehu population displayed the highest,up to 0.00651,while that between Lake Poyang and Lake Chaohu was the lowest to 0.00375.The fixation indices (F_st) of analysis of molecular variance (AMOVA) among populations was 0.0684,illustrating no significant population structure.The phylogenetic tree of cyt b built with MEGA 4.1 showed that five populations were not clustered into clades based on genetic distance.There was extensive general flow between yellow catfish populations from five lakes in the middle and lower reaches of the Yangtze River.