The Jardines de la Reina (JR) archipelago includes one of the largest marine protected areas (MPAs) in the Caribbean Sea. However, there is limited understanding about the assemblage structure of its coral reef fishes. We aim to (1) describe the spatial patterns of fish assemblages and their potential drivers along the reef system and (2) compare several metrics of assemblages inside and outside the MPA. We surveyed the ichthyofauna at 12 sites (inside and outside the MPA) along ~200 km of reef tract using a diver-operated stereo-video system. We identified 31323 fishes, represented by 95 species and 24 functional groups, including large rare and threatened species of parrotfishes and groupers. The biomass of fishes from the Lutjanidae, Serranidae, and Scaridae families was higher than that in other Caribbean reefs. Site and depth explained the larger fraction of variance in most of the evaluated metrics, suggesting the importance of local environmental heterogeneity. Fish assemblages did not show a significant gradient along the JR tract from the center of the MPA to the periphery. Distance to the center of the MPA explained some of the variability in the abundance, functional richness, and multivariate structure of assemblages. Our results do not show that fish assemblages inside the MPA are healthier than those outside. Instead, the ichthyofauna is abundant and both taxonomically and functionally diverse both inside and outside the MPA probably as a result of a spillover effect. The successful combination of natural and management-associated features likely results in an overall good ecological status of fish assemblages in JR.