) is one of the most important commercial freshwater species in China and, in recent years, its aquaculture has developed rapidly. However, with the expansion in cultivation scale, promiscuity and mixing between different populations has necessitated research on the genetic diversity of this species. A Japanese breed and Qingxi black mutant population are two new varieties of now found in China. Molecular research on these two new varieties is of great importance in the identification, germplasm protection and guidance of breeding studies on In this study, the 16S rRNA gene from 80 individuals of four populations (Yellow River, Japanese, Qingxi black mutant and Taiwan) of was amplified and sequenced for analyses of mutations, diversity parameters and s. A total of 53 mutation sites were detected in the studied gene including nine specific sites. A total of three specific sites were detected in the Qingxi black mutant population, one in the Japanese breed, one in the Yellow River population and four in the Taiwan population. The Qingxi black mutant population displayed the highest haplotype genetic diversity (0.821) followed by the Taiwan (0.484), Yellow River (0.195) and Japanese populations (0.100). The detected mutant sites added up to 16 haplotypes, including three in the Yellow River population, two in the Japanese, eight in the Qingxi black mutant and three in the Taiwan population. and genetic distance analyses showed a similar result in that the Yellow River and Qingxi black mutant population reflected a relatively closer relationship to the Japanese and Taiwan population, trees of haplotypes indicated that the four populations showed clear differentiation and can be identified effectively. The Japanese and Yellow River populations displayed a close relationship, indicating that the Japanese breed possibly originated in the Yellow River basin of China.