Clupeiform fishes are a globally critical group in supporting higher trophic levels and fisheries. Population scale studies of this group have focused on temperate species and found little variation. Tropical species have shorter, faster lives, and the impact of these key life history differences on observed genomic stock structure has not been investigated. We present data from sister species of tropical reef-based clupeiforms with differing spatial ecologies, Spratelloides delicatulus and S. gracilis. Sampling was performed along the Great Barrier Reef in a nested design of latitudes and reefs. We aimed to understand the spatial scale for genomic differentiation of “sprat” stocks and how spatial ecology, reef geomorphology and molecular diversity influences connectivity. The species share characteristics of demersal spawning and short lives but differ in habitat use. While both species have closer relations to coral reefs than true pelagics; S. delicatulus is common in shallow backreef waters, while S. gracilis is observed on reef slopes and surrounding waters. This contrast in environmental preference appears to have influenced the genomic structure and connectivity observed. We argue that reef fidelity, spawning behaviour and reef geomorphology play key roles in maintaining genomic diversity at small spatial scales; contrasting with results for temperate synonyms.