Blotched snakehead (Channa maculata) is an economically important aquaculture species in China and Southeast Asia, but wild blotched snakehead resources have declined sharply in recent years because of its overexploitation and habitat destruction. Thus, it is very urgent to develop genetic markers of blotched snakehead to investigate the natural resources. In this study, a total of 66 novel single nucleotide polymorphism (SNP) markers were developed based on 2b-RAD simplified genome sequencing. The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.130 to 0.667 and 0.112 to 0.502, respectively. The PIC ranged from 0.116 to 0.375. Two loci showed significant deviations from the HWE after Bonferroni correction (p < 0.05). These SNP markers will serve as a valuable tool for population genetic analysis, natural resource conservation and selective breeding of this blotched snakehead.