Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Dependent within Australia. Individuals are known to move between both countries, but it is disputed whether the stocks are reproductively linked. Accurate and unbiased determination of stock and population connectivity is crucial to inform effective management. In this study, we assess the genetic composition and population connectivity between Australian and New Zealand school sharks using genome‐wide SNPs, while accounting for non‐random kin sampling. Between 2009 and 2013, 88 neonate and juvenile individuals from Tasmanian and New Zealand nurseries were collected and genotyped. Neutral loci were analyzed to detect fine‐scale signals of reproductive connectivity. Seven full‐sibling groups were identified and removed for unbiased analysis. Based on 6,587 neutral SNPs, pairwise genetic differentiation from Tasmanian and New Zealand neonates was non‐significant (FST = 0.0003, CI95 = [−0.0002, 0.0009], p = 0.1163; Dest = 0.0006 ± 0.0002). This pattern was supported by clustering results. In conclusion, we show a significant effect of non‐random sampling of kin and identify fine‐scale reproductive connectivity between Australian and New Zealand school sharks.