Coral reefs are among the most biodiverse of coastal blue ecosystems, providing critical goods and services to millions of people worldwide. Despite their ecological and economical relevance, such biological systems have been experiencing dramatic decreases due to human-induced global and local stressors. Climate warming, pollution and overfishing are shifting the balance of many reefs, from coral to algal-dominated states. Central to coral reef functioning and resilience, herbivorous fishes graze on fleshy algae and contribute to nutrient cycling on reefs. Herbivory spans multiple functional groups – with distinct trophic niches and potential digestive strategies. How these groups associate with specific hindgut microbial communities, and how reef degradation reshapes these host-microbe relationships, remain poorly resolved. This is especially important given the role of gut microbes in fish health and fitness. Using 16S rRNA gene sequencing and standardised field sampling across herbivorous fish species, regions and reef conditions, we investigate how shifting coral reef states modulate the relationships between fish functional groups and hindgut bacterial communities. We examine regional patterns in alpha and beta diversity of fish hindgut bacterial communities from reefs across the Caribbean and Pacific spanning low to high macroalgal cover. More, we assess the relative contributions of biogeography, reef condition, and host identity (functional group, species) in shaping fish hindgut microbiota, as indicators of distinct digestive strategies. Bridging bacterial community dynamics with host ecology across coastal regions, this work contributes to a multi-scale understanding of blue ecosystems in transition.