An investigation was conducted on the genetic diversity of the hilsa fish in the major wetlands of Sylhet, with the objective of determining its linkage to populations from effectively maintained sanctuary regions. Field surveys and laboratory analyses, encompassing DNA extraction, PCR amplification, and cytochrome b sequencing, demonstrated genetic consistency among groups. Pairwise genetic differentiation (FST) values (0.000 to 0.017) demonstrated significant gene flow, corroborating the idea of a singular genetic pool. This genetic coherence highlights the feasibility of implementing established conservation techniques, including seasonal fishing prohibitions and the creation of sanctuaries, in Sylhet. The results underscore the significance of genetic knowledge in sustainable fisheries management and biodiversity preservation. By implementing these measures, the Sylhet region can augment hilsa production, bolster ecological services, and elevate the livelihoods of local populations. This study establishes a framework for integrating Sylhet into the national fisheries narrative, in accordance with global conservation objectives.