Single nucleotide polymorphism (SNP) is one of the commonly used molecular marker-assisted breeding tools. In this study, based on the high-density linkage map and QTL mapping results of black carp (Mylopharyngodon piceus) in previous study, two SNP molecular markers at the body weight QTL interval were used to verify in three populations. The purpose of this study was to verify whether the SNP from previous study exists and can be applied to other geographic groups. Two SNP molecular markers flanking sequences were analysed by using performing genotype composition analysis, genetic diversity analysis and neutrality test in three geographic groups. The results of genetic diversity showed that the haplotype diversity (H_d) of the extended fragment of snp8107 was 0.782, 0.515 and 0.497 in Hanjiang population, Xiangjiang population and Shishou population, respectively; the observed heterozygosity (H₀) of each locus was from 0.067 to 0.533; The expected heterozygosity (H_e) ranged from 0.127 to 0.506, with an average of 0.306, and the polymorphic information content (PIC) ranged from 0.117 to 0.374, with an average of 0.246. The neutral test for three populations showed that the bottleneck effect may have occurred in history which led to loss of the rare alleles. Combined with the results of genetic diversity, we speculated that the Hanjiang population retained more rare alleles after experiencing the bottleneck effect. It was concluded that the Hanjiang population was the best variety suitable for genetic improvement.