Abstract: Channa maculata is not only an indigenous economic fish in South China but also a parent species of cultured hybrid snakehead. Escape of the bred individuals may have impacts on wild populations, which makes genetic background analysis of wild resources an urgently need. This study analyzed the distribution characteristics of microsatellite markers in genome of C. maculata, and developed 20 polymorphic loci to analyze the genetic diversity and genetic structure of six wild populations named as Guangzhou, Huazhou, Jianghua, Nanning, Yangjiang and Shaowu populations. The results show that the number of alleles (N_a) of the six wild populations was 3−28; the number of effective alleles (N_e) was 1.28−14.88; the observed heterozygosity (H_o) was 0.10−1.00; the expected heterozygosity (H_e) was 0.14−0.95; the polymorphic information content (PIC) was 0.13−0.95. The UPGAM dendrogram indicates that the genetic relationship between Huazhou and Fujian populations was the closest, but that  between Huazhou and Jianghua populations was the farthest. This study provides basis for the conservation and management of germplasm resources of C. maculata.