Marine protected areas (MPAs) have been implemented on coral reefs as management and conservation tools since coral reefs provide significant ecological and economic values. For instance, Punta Francés National Park (PFNP) constitutes one of the most pristine marine environments in the Cuban archipelago, where recreational SCUBA diving has long been the most important activity. The goods and services provided by this area, the gaps in its biodiversity knowledge, and the putative effect of the MPA, prompted this research aims (1) to characterize reef fish assemblages in the coral reef of Punta Francés and (2) to test the hypothesis that PFNP hosts more abundant and diverse fish assemblages than the adjacent non-protected reef due to the higher habitat heterogeneity and protection level inside the PFNP. We have organized the analysis into four parts: (1) taxonomic and functional variation of fish assemblages; (2) potential factors influencing fish assemblage structure; (3) representativeness of species with special concern; and (4) functional redundancy analysis. The study was carried out from 2011 to 2014 in three reef habitats (reef crest, reef slope, and spur and groove), both inside and outside the PFNP. We found no differences in species and functional composition of fishes between areas with different protection levels. However, reef fish assemblages depended heavily on habitat type, demonstrating the importance of reef slope and reef crest habitats. No strong mangrove-seagrass bed-coral reef connection was evident for the ichthyofauna reported to use mangroves and seagrasses as nurseries. Low biomass and abundance of predatory species and fish families important to conservation is a concerning outcome. Some functional traits were represented by only one or very few species across the entire area, which likely compromised ecological function in the system. The most distressing issue was the non-consistent differences found between protected and non-protected areas, suggesting the necessity of reviewing the management objectives for reef fishes in PFNP and a clear need to update its management plan and perhaps its boundaries.