The Channa genus includes important species for aquaculture and interesting targets for phylogenetic studies. In the Mekong Delta, Viet Nam, four species of this genus (Channa striata, C. micropeltes, C. lucius, and C. gachua) are naturally distributed and other phenotypes that look like C. striata have been observed in aquaculture conditions. The taxonomic status of newly-observed phenotypes including “triangle-head” snakehead (THS) and square-head snakehead (SHS) is still controversial. This study compared morphological characteristics and Cytochrome C oxidase subunit I (COI) sequences of different C. striata-like phenotypes and investigated the phylogenetic relationship of Channa species based on COI. Morphological results show that THS, SHS, and wild C. striata have similar ranges for meristic traits but differ in morphometric ratios, especially the shape of their head and length of their gut. Kimura-2P genetic distances among three phenotypes (0.0017-0.0062) are equivalent to those ofC. striata samples from Mainland Southeast Asian countries. The results indicate that THSand SHS belong to C. striata, and this species exhibits within-species diversity in both morphology and COI sequences. The phylogenetic analysis indicates that C. striata individuals form a monophyletic group and are genetically distinct from other Channa species in the Vietnamese Mekong Delta. Congeneric distances of four species range from 0.1836 to 0.2436, indicating high divergence among Channa species.