The brown-banded bamboo shark, Chiloscyllium punctatum is one of the most common shark species caught in coastal fisheries throughout the Indo-Malay region and the most abundant shark caught in trawl fisheries in Malaysia and Thailand. Differences in fisheries regulations related to trawling among jurisdictions, and an absence of either stock assessments or population estimates in the region, raise questions about the sustainability of fisheries that take this species. As a small-bodied, benthic shark that predominantly inhabits shallow, soft substrate habitats, the population may be particularly vulnerable to trawling throughout the region. We investigated the population structure of Chiloscyllium punctatum using genome-wide nuclear markers. Comprehensive DNA sampling was undertaken in Thailand, Malaysia and Indonesia, and population structure analysis using SNP datasets revealed at least four genetically distinct regional groups of C. punctatum. We identified a potentially shared stock between Malaysia and Indonesia, and separate populations in the Andaman Sea off Thailand, the South China Sea, and a localized population in South Sulawesi, Indonesia. Each of these stocks may likely require different management approaches tailored to the scale and types of fishing pressure in the different regions.