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The Australian gummy shark Mustelus antarcticus is distributed across southern and eastern Australian waters and is the main target of a large shark fishery. Commercial harvest of the species is considered sustainable based on biomass estimates that show recovery from past overexploitation. However, the effective population size and genetic-based assessments of stock structure remain unresolved. We evaluated the genetic structure and effective population size (Ne) of the gummy shark using genome-wide single nucleotide polymorphisms. We found genetic divergence between individuals from the east coast and those along the south coast, resulting in 2 discrete populations with signatures of adaptive divergence. Spatial analyses revealed widespread gene flow within each of these populations, with some evidence for mild isolation-by-distance observed using individual-based tests. Demographic modelling of each population showed a comparatively rapid decline of Ne in the most recent past compared to more historical projections, with evidence that such declines have occurred to the point where genetic variation could be at risk. The identification of 2 divergent populations of gummy shark suggests that management should consider each individually to ensure the long-term sustainability of the species.