Snapper (Pagrus auratus) collected from the Eastern Gulf, Denham Sound and Freycinet Estuary areas of Shark Bay were used to investigate spatial variation in life history characteristics including maximum age, growth, maturity and spawning time. The peak spawning period occurred at different times in each area and varied in duration. Maximum observed ages were 17 years in the Eastern Gulf and Denham Sound compared with 31 years in the Freycinet Estuary. There were significant differences in both length and age at maturity between sexes within each area and for both sexes among areas. Sex-based differences in growth within areas were not significant, however, when lengths at age were pooled and compared among areas, growth in Denham Sound was significantly different to that in the Eastern Gulf and Freycinet Estuary. This fine-scale variation in life history characteristics, while unusual for a large, potentially mobile sparid, inhabiting a marine environment with no obvious physical barriers, is linked to the Bay’s marked environmental heterogeneity, low levels of mixing and historic differences in fishing pressure. Results are consistent with previous stock identification studies and add further support for the geographic scale at which local snapper stocks and the recreational fishery are managed.