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Abstract Obtaining reliable estimates of the effective number of breeders (Nb) and generational effective population size (Ne) for fishery‐important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single‐cohort young of the year and mixed‐age adults from two geographically and genetically isolated stocks of the Australasian snapper (Chrysophrys auratus) to investigate the feasibility of generating reliable Nb and Ne estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome‐wide SNPs and the linkage‐disequilibrium method, we determined that the most reliable Nb and Ne estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed‐age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating Nb and Ne for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery‐important species.

Abstract The efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper (Chrysophrys auratus) along ~2600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight sampling locations to characterize population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbour. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity were uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid‐west and south‐east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on‐shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, indicating the likely benefits of a review. This study supports the value of population genomic surveys in informing the management of weakly structured and wide‐ranging marine fishery resources.