This study was undertaken to determine the genetic variability and phylogenetic relationship of four channid species (Channa punctatus, C. marulius, C. striatus and C. gachua) from the family Channidae, using mitochondrial cytochrome b gene. A 309 bp segment of the cytochrome b gene was sequenced and analysed for intra-specific and inter-specific sequence variations. Channa marulius has the highest genetic similarity (98.55%) while C. gachua with minimum overall similarity (94.78%) is displaying the highest genetic variability. The maximum inter-specific similarity was observed between C. marulius and C. striatus (84.15%), hence phylogenetically more akin to each other and grouped into the same clade. Channa gachua and C. striatus are found most distantly related to the lowest inter-specific similarity of 77.58%. Phylogeny reconstruction using UPGMA, Minimum Evolution and Neighbour Joining methods generated a similar tree. Intra-specifically, C. punctatus and C. marulius showing a considerably greater degree of similarity suggest a tendency of their genome homogenization which makes these species vulnerable to environmental stresses. The data suggests that urgent steps need to be taken to conserve C. punctatus and C. marulius by initiating specific conservation strategies and suitable breeding programs to enhance their genome heterogeneity which may make these species hardy to withstand environmental vagaries.