<p>The structural complexity of reef habitats is known to promote higher functional diversity in associated assemblages, including fish. However, amidst increasing coral bleaching events and massive coral mortality in the Mexican tropical Pacific, it is crucial to evaluate how the structural complexity of these reefs influences the fish functional diversity to strengthen restoration and conservation strategies for the structural recovery of these ecosystems. This study evaluated changes in fish functional diversity between coral ecosystems with different reef development (coral communities vs. coral patches). Local alpha functional diversity was estimated using multidimensional indices and functional dissimilarity (β) between fish assemblages. The results show significant differences in fish functional diversity between reef development conditions. Sites with coral communities (rocky reefs with isolated coral colonies) presented higher values of species richness, abundance, biomass, and functional diversity, particularly in functional richness and functional divergence. Sites with monospecific coral patches had the highest differentiation, with high values of beta functional diversity and functional turnover as the most important component. These findings indicate that the coral structure’s condition influences the functional diversity of fishes, i.e., the high structural complexity of the habitat favors high taxonomic diversity and functional alpha diversity. While coral communities are important habitats for the local taxonomic and functional diversity of fishes, coral patches also contribute significantly to functional connectivity. Hence, both habitats should be included in conservation efforts for these ecosystems.</p>