During the non-breeding season (September–April), Black-tailed Godwits (Limosa limosa) are commonly seen in coastal and inland wetlands of the Ganges-Brahmaputra-Meghna Delta in Bangladesh. We hypothesize that the Ganges-Brahmaputra-Meghna Delta, at the overlap between the Central Asian and East Asian–Australasian flyways, may host three subspecies that breed in disjunct areas of temperate and northern Asia: L. l. limosa, L. l. melanuroides, and L. l. bohaii. We used mitochondrial DNA (mtDNA) haplotype network and biometric analysis to determine subspecies in captured individuals, and deployed GPS–GSM transmitters to verify breeding areas of individuals with subspecies assignments. To test for differential habitat preferences, we sampled birds at two ecologically distinct habitats known to host the largest concentrations of non-breeding Black-tailed Godwits in Bangladesh: Nijhum Dweep National Park, a tidal coastal habitat with brackish water on the south-central coast, and Tanguar Haor (‘backmarsh’), a seasonal freshwater floodplain in the north. During the non-breeding seasons of 2021–2022 and 2022–2023, we sampled and measured 93 Black-tailed Godwits, 54 of which were equipped with GPS–GSM transmitters. Our mtDNA haplotype network analysis confirmed the presence of limosa, melanuroides, and bohaii subspecies at the study sites. Thus, indeed, Black-tailed Godwits subspecies, despite having distinct breeding ranges, exhibit (partially) overlapping non-breeding ranges in Asia. The subspecies composition differed significantly between sites, with limosa and bohaii dominating in Tanguar Haor and melanuroides in Nijhum Dweep. Of the 21 individuals that were tracked to their breeding grounds, 18 migrated to the expected breeding range of their respective subspecies. However, one bird with a limosa haplotype migrated to a known breeding area of bohaii, whereas two birds with melanuroides haplotypes migrated to the supposed breeding range of limosa. Therefore, while ecological factors at both ends of the flyways may shape the morphological and behavioural differences between Black-tailed Godwit subspecies, their delineations and possible gene flow require further studies.