Understanding the underlying drivers of biodiversity is essential for conservation planning of large, connected seascapes. We tested how patterns in alpha and beta components of species and functional diversity of coral reef fish (214, species, 23 families) varied along the extensive Chagos Lakshadweep oceanic ridge (the largest chain of mid-oceanic atolls in the Indian Ocean) and evaluated geomorphological, environmental, and anthropogenic predictors of diversity patterns. alpha and beta diversity (species and functional) showed contrasting patterns along the ridge; richness and alpha diversity decreased towards the north and were influenced by anthropogenic pressures, while beta diversity increased towards the north, along environmental gradients and with geographic distance. Species beta diversity was dominated by turnover (> 80%), while functional beta diversity was dominated by nestedness (> 60%). Geographically distant reefs (> 2000 km apart) with high structural complexity were functionally similar, illustrating a ridge-wide capacity for reefs to maintain ecological structure and function despite significant differences in biodiversity. Low spatial congruence in different facets of biodiversity suggest differentiated management needs for reef fish communities along the Chagos-Lakshadweep ridge. Specifically, while a single large marine reserve may be effective for biodiversity conservation in the Chagos archipelago in the south, a network of several smaller conservation areas may be needed to confer resilience to densely populated and biologically differentiated reefs further north.