The great snakehead, Channa marulius, is distributed across its natural distribution range of Southern and Southeast Asian countries. This valuable fish individual is endangered in Bangladesh, and its availability becomes limited only during winter which needs to be conserved, and no information has been recorded regarding the populational variations. In the current study, mitochondrial cytochrome b (Cytb) and cytochrome oxidase subunit 1 (CO1) genes were amplified and sequenced collecting samples from seven geographically distinct low-land ecosystems in Bangladesh. The amplification size was 742 (Cytb) and 558 (CO1) bp, and 10 and 11 haplotypes were found, respectively. Populations from Barishal, Sylhet, Mymensingh and Chattogram showed private haplotypes for both genes. The Cytb gene had the highest haplotype diversity (0.80) in the Mymensingh population, while the CO1 gene had the highest haplotype diversity (0.75) in the Rajshahi population. The Fst value showed the highest between Dhaka vs. Sylhet (0.912) in the case of the Cytb gene; whereas, the highest Fst value was recorded in Rajshahi vs. Sylhet, and Barishal vs. Sylhet (0.67) for CO1 gene, with a significance level of P≤ 0.05 for both genes. The phylogenetic tree constructed by both Cytb and CO1 genes produced three groups: Bangladeshi, shared with Indians, and shared with Pakistani strains.  Finally, mtDNA genes identify a close but diversified relationship with the South Asian countries C. marulius species. Besides, several diversified groups were identified among Bangladeshi stripped snakehead populations that need to be carefully conserved for further extinction may happen.