Objective  This study aims to analysis the genetic diversity of Cyprinidae in South China, and provide reference for genetic breeding of freshwater fish.

Methods  The genetic diversity of Cyprininae fish in South China, a total of 156 samples from six populations of four species of Cyprininae fish, including Cyprinus carpiorubrofuscus Lacepede, Cyprinus acutidorsalis Wang, Cyprinus multitaeniata Pellegrin et Cheveyand, Carassioides cantonensis Heincke, were collected in Hainan Province, Guangdong Province, and Guangxi Zhuang Autonomous Region. The mitochondrial D-loop marker was used to analyze genetic diversity.

Results This study showed that the genetic diversities of Cyprinus carpio rubrofuscus Lacepede had higher genetic diversity. In which, the haplotype diversities based on D-loop were 0.814, 0.895 and 0.879, respectively. The haplotype diversities of Carassioides cantonensis Heincke, Cyprinus acutidorsalis Wang and Cyprinus multitaeniata Pellegrin et Chevey based on D-loop were in lower levels, which were 0.748, 0.794 and 0.536, respectively. Among which, the genetic diversity of Hainan population was lower a bit than that of the Pearl River population and Rongjiang population. This may be caused by the Ice Age and the separation of Qiongzhou Strait. The genetic diversities of Carassioides cantonensis Heincke, Cyprinus acutidorsalis Wang and Cyprinus multitaeniata Pellegrin et Chevey were in very low levels, which were related with their small distributions and low viabilities. This study found that Cyprinus acutidorsalis Wang, Cyprinus multitaeniata Pellegrin et Chevey, and Carassioides cantonensis Heincke did not share any haplotypes, indicating that there was no recent population exchange among these three taxa and suggesting significant population differentiation. Additionally, Cyprinus multitaeniata Pellegrin et Chevey and Carassioides cantonensis Heincke did not share haplotypes with Cyprinus carpiorubrofuscus Lacepede, indicating that there was no recent genetic exchange between these two taxa and Cyprinus multitaeniata Pellegrin et Chevey and Carassioides cantonensis Heincke have been separated from the population of Cyprinus carpiorubrofuscus Lacepede for a relatively long period of time.

Significance This research provides important insights into the natural resource status of Cyprinidae fish in South China and offers a reference for future conservation and genetic breeding.