The adult anadromous hilsa shad (Tenualosa ilisha) live in the Bay of Bengal and migrate to the estuaries and freshwater rivers for spawning and nursing of the juveniles. This has led to two pertinent questions: i) do all hilsa shad that migrate from the marine to freshwater rivers come from the same population? and ii) is there any relationship between adults and juveniles collected from the same sampling sites?In order to address these questions, NextRAD sequencing was applied to genotype 14,894 quality filtered single nucleotide polymorphism (SNP) loci for 180 individuals (both juveniles and adults) collected from six strategic sampling sites, consisting of freshwater riverine, brackish water estuarine and marine habitats. This broad clustering of hilsa shad populations in turn mirrors the divergent local adaptations in differing environmental habitats influenced by turbidity and salinity levels such as turbid freshwater (Western Riverine), clear freshwater (Eastern Riverine) and brackish-saline (Southern Estuarine-Marine).