The yellow catfish (Pelteobagrus fulvidraco) is extensively distributed throughout rivers and lakes of China. With overexploitation and water eco-environment deterioration, the resources of P. fulvidracao are severely affected. The genetic diversity and population structure of the commercial fish were examined by using 413 bp of the first hypervariable region of mitochondrial DNA sequences in 258 specimens collected from 9 localities in China. Only 18 polymorphism sites were detected and 22 haplotypes were defined. All of the 9 populations exhibited middle-low haplotype diversity and low nucleotide diversity (h=0.336±0.095~0.700±0.078; π=0.087±0.096%~0.258±0.208%). Low genetic differentiation was estimated within Yellow River deme and Yangtze River deme and significant level of genetic structure was detected between two drainages via AMOVA and pairwise F_ST. The uncertainty of genetic structure in Sheyang River and Hongze Lake populations may be connected with the extensive gene flow between the two populations and the two drainages especially during 1128-1855 AD. Neutrality tests, analysis of mismatch distribution and Bayesian skyline analysis suggested that all populations and Yangtze River deme experienced historical sudden and special population expansion. The climatic changes in the Quaternary may have had an important influence on P. fulvidraco and climate warming during the last interglacial age may have played an important role in population expansion. Information on genetic diversity and genetic structure will have implications for the management of fisheries and conservation efforts.