Onshore to offshore gradients in marine assemblages have been well documented on coral reefs, with most studies showing a distinct separation between onshore and offshore locations. Here we use enclosed anaesthetic sampling of small, cryptobenthic reef fishes to assess changes in assemblage composition across the Great Barrier Reef continental shelf. The cryptobenthic fishes exhibited fine-scale partitioning across the shelf. Three dominant species of goby accounted for over 55% of all fishes collected, with 1 species characterising each of the 3 key shelf positions: inner-, mid- and outer-shelf. Multivariate analyses of assemblage composition revealed further separation of reefs within the inner- and mid-shelf positions, highlighting the exceptional sensitivity of cryptobenthic reef fish assemblages to shelf position, with a progressive separation of individual reef assemblages with distance from the shore. These among-reef patterns contrast markedly with other reef fish taxa which invariably show 2 broad assemblages across the continental shelf (inner- vs. a composite mid- and outer-shelf community). As a result of this exceptional sensitivity to environmental conditions, cryptobenthic reef fish communities may represent good subjects for high-resolution monitoring of disturbances on coral reefs.