Knowledge of community structure within an ecosystem is essential when trying to understand the function and importance of the system and when making related management decisions. Within the larger ecosystem, microhabitats play an important role by providing inhabitants with a subset of available resources. On coral reefs, cryptobenthic fishes encompass many groups and make up an important proportion of the biodiversity. However, these fishes are relatively small, exhibit extreme visual or behavioral camouflage, and, therefore, are often overlooked. We examined the differences in fish community structure between three common reef microhabitats (live hard coral, dead coral rubble, and sand) using ichthyocide stations in the central Red Sea. Using a combination of morphological and genetic (cytochrome oxidase I (COI) barcoding) techniques, we identified 326 individuals representing 73 species spread across 17 families, from fifteen 1 m quadrats. Fish assemblages in the three microhabitats were significantly different from each other. Rubble microhabitats yielded the highest levels of fish abundance, richness, and diversity, followed by hard coral, and then sand. The results show that benthic composition, even at a small scale, influences cryptobenthic communities. This study also provides new COI sequence data to public databases, in order to further the research of cryptobenthic fishes in the Red Sea region.