Clupeiform fishes are a critical group in supporting higher trophic levels and commercial fisheries. Temperate clupeiformes have been intensely studied, however tropical species have been relatively ignored. The objective of this study was to use ecological and genetic approaches to elucidate the hierarchical population structure among a group of tropical clupeiformes on the Great Barrier Reef. The common tropical sprat Spratelloides delicatulus was sampled over multiple year. All life stages were most abundant within the lagoons of reefs when compared to inter-reefal waters; suggesting a strong degree of reef association in comparison with previous open water assumptions. Population genetics of S. delicatulus suggested separate stocks of this tropical clupeiform over spatial scales greater than 800km. Variation in size to maturity and patterns of growth correlated with genetic differentiation over broad spatial scales concurring with our conclusion of stock structure. Surprisingly, genetic substructure was found between reefs separated by 10s of kms in the Capricorn Bunker. We argue that reef fidelity, spawning behaviour and reef geomorphology play a role in maintaining higher levels of genetic diversity.  Our results for tropical sprats contrast with patterns for temperate clupeid that generally have well mixed stocks over scales in excess of a 1000km.