Benthic mobile invertebrates are important components of coral reef diversity and community structure, although in most cases their ecological contributions are poorly known. The objectives of this study were 1) to describe diversity and composition patterns of epibenthic mobile invertebrate assemblages in shallow-water coral reef communities in Florida and 2) to evaluate these animals’ ecological roles by reviewing publications on their diet. Underwater surveys were conducted during the summer of 2013 at 40 sites distributed along the Florida Reef Tract from Broward County to the Dry Tortugas. The survey data included 618 records of 116 unique morphospecies, representing 83 species from 61 genera, 46 families, 19 orders, seven classes, and four phyla of mobile invertebrates comprising herbivores, detritivores, carnivores, omnivores, and suspension feeders. Of the identified taxa, six were recorded at the majority of the sites (≥50 % of sites), while 43 taxa were encountered only once. Nearly ubiquitous taxa were the snapping shrimp Alpheus armatus, red reef hermit crab Paguristes cadenati, and long-spined urchin Diadema antillarum. Each reef type was characterized by assemblages of dominant taxa: echinoderms were the most diverse in patch reefs and the Southeast Florida Reef Complex, molluscs were most diverse in shallow bank reefs, and arthropods were most diverse in deep bank reefs and the Southeast Florida Reef Complex. These results suggest that reef habitats are characterized by distinct communities of fauna, and that individual phyla and feeding guilds possess mostly unique but overlapping habitat requirements. This study establishes a reference point for further research and monitoring of ecological changes to inform conservation strategies for the Florida reef systems.