Evaluating the structure of fish assemblages(the number and abundance of different fish species in a given body of water)can be used to assess reef health, environmental quality ,and change, which is critical as tropical reefs face unprecedented pressures from human-derived sources. The structure of invertebrate (invertivore) and fish-feeding (piscivore) species groups, called trophic guilds, were assessed in relation to coral and sandstone reef habitat types within the Trincomalee Bay area. Variation in the physical parameters of reef habitats can alter the amount of shelter and food available, influencing the diversity and abundance of reef fish communities. Species richness (number) was positively influenced by several habitat types, while abundance showed no correlation with habitat type and nor did two-way interactions between the guild and habitat type. Diversity of fish assemblages was not correlated with differences in reef habitat type. Observationally, the reef habitat types showed variation in structural complexity, live coral cover, diversity of coral species, and proportion of coral, coral rubble and sandstone. Understanding the physical characteristics of tropical reef habitats that promote diversity and abundance of reef fish assemblages and how fish-habitat interactions influence the structure of these assemblages is critical for the maintenance of ecosystem functioning and the protection of these vulnerable ecosystems. This study not only highlights the fish-habitat interactions on unique sandstone reef habitat types ,but also adds to the sparse literature regarding the Trincomalee Bay area and moves towards a better understanding.