Channa maculata, an economically significant freshwater fish in China, has been subject to a limited number of population studies. To explore the genetic diversity of naturally distributed populations of C. maculata, single nucleotide polymorphism (SNP) markers were developed and genetically analyzed in seven populations (Yangchun, Guangdong; Huazhou, Guangdong; Nanning, Guangxi; Hezhou, Guangxi; Jianghua, Hunan; Shaowu, Fujian; Taipei, Taiwan) using the simplified genome sequencing technology of SLAF. The findings revealed the detection of 2502887 SNP loci, with an average sequencing depth of 20.19×, and average Q30 and GC contents of 95.31% and 41.16%, respectively. Population genetic structure analysis revealed individual clustering of all seven populations, each with a distinct genetic structure. The polymorphic information content of the seven C. maculata populations was 0.2672–0.2872, the expected heterozygosity (H_e) was 0.3304–0.3580, and the observed heterozygosity (H_o) was 0.2145–0.3393. The populations had a medium level of genetic diversity. The genetic differentiation index (F_st) was 0.15300–0.78658 and the gene flow (N_m) was 0.24118–0.62035, showing a medium-high genetic differentiation status among populations. Phylogenetic analysis revealed that the Hezhou population was most closely related to the Jianghua population. Given their close geographical proximity in Guangxi and Hunan, the Hezhou and Huazhou populations can be considered part of the same population unit. The Taibei group exhibited the smallest differences in H_e and H_o, indicating a high degree of genetic purity. Conversely, both the Hezhou and Huazhou groups displayed lower H_o than H_e and substantial differences. Furthermore, the seven populations exhibited high genetic differentiation from each other, with the Taipei group showing extreme differentiation, likely due to the strait’s isolation effect. This study elucidated the genetic background and relationships among wild C. maculata populations across various regions, and serves as a valuable reference for the strategic utilization of spotted snakehead germplasm resources and genetic breeding endeavors. Particular emphasis should be placed on introducing new lineages in future breeding efforts to enhance genetic diversity within C. maculata populations and facilitate the rational exploitation of C. maculata germplasm resources.