The great northern snakehead, white type Channa argus is one of the most important economic and conservational fish in China, but an uncertain classification has existed for many years. In present study, mitochondrial Cyt b gene was used to analyze the relationships and genetic diversity of two color morphs of northern snakehead. For the Chnannidae family, the average genetic distances of Cyt b gene was 0.171 (ranged 0.000 to 0.248) with the inter-species genetic distances. The intra-species genetic distance ranged from 0.000 to 0.002. For the haplotypes of two color morphs of Channa argus, the mean pair-wise genetic distances were estimated as 0.002, which were within the intra-species genetic distance interval for Channa species, indicating that they belonged to the same species, but not subspecies at the molecular level. Moreover, take Lateolabrax maculates and Epinephelus coioides as outgroups, molecular phylogenetic tree showed that all the haploids gather together as a branch and crossing each other. These indicated that the white type Channa argus should be regard as an albino of biocolor type.