The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise F_ST values ranged from 0 to 0.5530. Among these, high F_ST values (0.1931–0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20–30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.

This study examines the genetic diversity and population structure of silver carp (Hypophthalmichthys molitrix), an ecologically and economically important freshwater species. Samples were collected from 17 sites along the Yangtze River, including LCH, LCS, LJHK, and LXZX, as well as one population from the United States (SV). Restriction-site associated DNA sequencing (RAD-seq) generated 759,453 high-quality single-nucleotide polymorphisms (SNPs) for population genomic analyses, including genetic differentiation (F_ST), population structure, and linkage disequilibrium (LD) decay. Genetic variation was primarily found within populations (78.05%), with 21.94% among populations. Most sites exhibited low genetic differentiation (F_ST < 0.05), suggesting high admixture along the river, although a few sites displayed elevated values (F_ST > 0.15). Rapid LD decay in LCH, LCS, and LJZ indicated frequent recombination and moderate to large effective population sizes. These patterns reflect the influence of geographic and ecological factors on population structure. Conservation strategies should maintain genetic connectivity while protecting distinct genetic resources. Populations with high differentiation, such as LXZX and LWZ, warrant targeted management to preserve unique genetic diversity.