The anadromous hilsa shad (Tenualosa ilisha) is a commercially and ecologically important fish species distributed across the Bay of Bengal, the Arabian Sea, and the river systems of South and Southeast Asia and the Middle East. Despite its significance, the genetic diversity, population structure, and demographic history of T. ilisha populations are poorly understood, particularly across the regions. This study provides the first comparative genetic analysis with extensive sampling of T. ilisha populations from Bangladesh and Iraq, utilizing mitochondrial DNA markers—Cytochrome c Oxidase I (COI) and Cytochrome b (CYTB)—to assess genetic variation, population connectivity, and evolutionary history. Genetic analyses of 278 COI and 268 CYTB sequences revealed significant inter-regional genetic differentiation, with Bangladeshi populations exhibiting higher genetic diversity, while Iraqi populations displayed extreme genetic homogeneity. Population structure analyses using analysis of molecular variance and F-statistics (Fst) demonstrated strong genetic differentiation between Bangladeshi and Iraqi populations, with inter-regional variation accounting for over 65% (COI) and 73% (CYTB) of the total genetic variation. Intra-regional differentiation was low among Bangladeshi populations, suggesting gene flow and a largely panmictic population structure, whereas Iraqi populations showed no significant genetic differentiation, indicating a single, genetically uniform stock. Haplotype network analyses supported inter-regional isolation and intra-regional connectivity, with no shared haplotypes between Bangladesh and Iraq. Neutrality tests (Tajima’s D and Fu’s Fs) suggested recent demographic expansions in several Bangladeshi populations. Conversely, Iraqi population the Shatt al-Arab showed little sign of expansion. The results underscore the need for region-specific conservation measures. Preserving ecological integrity and sustainable fisheries management in Bangladesh and habitat degradation mitigation and restoration in Iraq are important to avoid further loss of genetic diversity. Future studies should integrate genomic analysis and environmental monitoring for T. ilisha across its distribution so that adaptive management practices can be developed.