Analysis of genetic diversity and population structure of the yellow catfish (Pelteobagrus fulvidraco), an important commercial aquaculture species that is widely distributed throughout China's fresh waters, could contribute to scientific management and sustainable utilization of this species. To characterize the population genetic structure of yellow catfish across China, 448 individuals from 10 locations across North, Central, and South China were analyzed using 15 microsatellite loci. Moderate to high genetic diversity was determined in all nine natural populations, while genetic diversity was slightly lower in the cultured populations. Two subgroups were detected, indicating clear genetic differences among the natural populations in China. This research represents the first comprehensive study of the genetic diversity of yellow catfish throughout its entire Chinese range, and the results may inform effective fisheries management and systematic selective breeding of the yellow catfish.