In order to explore the genetic diversity and structure of total female yellow catfish (Tachysurus fulvidraco) population, and compare the genetic differences between cultured and wild populations, this study studied the genetic diversity of all-female (AF), wild (LH) and other cultured populations (WH, QJ, YX, JM, JZ, etc.) of yellow catfish in Hubei Province. A total of 210 individuals from 7 populations of yellow catfish were sequenced and their genetic diversity and structure were compared. The results showed that nucleotide diversity (ND), average polymorphism information content (PIC), average observed heterozygosity (Ho) and expected heterozygosity (He) in all-female populations were 0.000 5, 0.046 9, 0.052 5 and 0.046 9, respectively. In wild populations, ND, PIC, Ho and He were 0.001 7, 0.178 4, 0.197 4 and 0.178 4, respectively, while in other cultured populations, they were 0.000 6, 0.047 7, 0.052 4 and 0.047 7, respectively. The ND, PIC, Ho and He of wild female population were 0.004 1, 0.302 2, 0.508 3 and 0.352 3, respectively, and the mean values of female population in cultured population were 0.000 6, 0.047 3, 0.052 2 and 0.047 3, respectively. The genetic diversity of the all-female population was not significantly different from that of the other five cultured populations, and was significantly lower than that of the wild population. The results of phylogenetic tree and principal component analysis (PCA) showed that there were individuals closely related to wild population and other cultured population, and some individuals from cultured population and wild population also had similar genetic backgrounds. These results indicate that the genetic diversity of whole female and cultured populations is close to each other, but lower than that of wild populations, suggesting that it is particularly important to improve the genetic diversity of female parents in future breeding.