Abstract: The Labeoninae subfamily consists of small to medium-sized fish within the Cyprinidae family that are adapted to flowing water environments and feed mainly on algae. They are widely distributed across tropical and subtropical regions of Asia and Africa. In China, the primary cultured species include Cirrhinus molitorella, C. mrigala, Labeo rohita, and Bangana decora. In recent years, influenced by environmental and ecological pressures, their suitable habitats have been continuously shrinking, making genetic resource assessment and conservation urgently needed. Existing studies have shown that there is certain genetic differentiation among C. molitorella populations from different river systems, with wild populations exhibiting higher genetic diversity than cultured groups. Compared to traditional markers, SNP markers offer advantages in throughput, coverage, and stability, enabling more precise analysis of population genetic structure. Therefore, this study aimed to assess the current genetic status of germplasm in four cultured fish species of the subfamily Labeoninae. A total of 53 fin samples were collected from three wild populations (C. molitorella from Guangdong, C. molitorella from Guangxi, and B. decora) and two cultured populations (C. mrigala and L. rohita). Genomic DNA was extracted from the samples, and subsequent detection was conducted using a liquid-phase microarray. Rigorous quality control and filtering were performed on the raw data to screen out high-quality single nucleotide polymorphism (SNP) loci, which were then used for the analysis of genetic diversity and population structure, including the evaluation of indicators such as fixation index (F_st) and nucleotide diversity (π). A total of 331 750 080 Clean Reads were obtained, and 28 693 SNP loci were detected. The nucleotide diversity (π) of the four Labeoninae species ranged from 0.000 003 54 to 0.000 020 75, and the genetic differentiation coefficient (Fst) among populations varied from 0.018 to 0.554, indicating significant genetic differentiation among different species. Phylogenetic tree construction, principal component analysis (PCA), and STRUCTURE-based clustering analysis consistently revealed that the four Labeoninae fish populations were clustered into two distinct groups:C. molitorella, L. rohita, and C. mrigala hybrid formed one cluster, while B. decora formed a separate cluster. Additionally, the wild populations of C. molitorella from Guangdong and Guangxi exhibited relatively low levels of genetic diversity, accompanied by significant genetic differentiation between the two geographically isolated populations. Therefore, to conserve wild germplasm resources and enhance the genetic diversity of farmed populations, conservation management should be implemented, including restoring gene flow among different river system populations and preventing inbreeding depression, thereby strengthening the protection and sustainable utilization of C. molitorella wild germplasm resources.