Microbial communities inhabiting marine waters are compositionally unique with distinct metabolic profiles. These assemblages are important drivers for biogeochemical cycles and impact ecosystem function. Changes to environmental systems impact the diversity of local microbiota as well as the macroorganisms. Several examples in nature illustrate reduced diversity and trophic connectivity caused by human activities; though it remains unclear how the loss of microbial diversity and associated function impacts ecosystem stability. Here, we examine marine microbial community structure and diversity on coral reefs across 11 inhabited and 16 uninhabited Pacific Islands and Atolls. Metagenomic sequence analysis was used to compare the community composition and metabolism at 81 reef sites. The results demonstrate that microbial community diversity is diminished at inhabited locations primarily by a loss of evenness. The structure of these marine microbial communities was differentiated by rank abundance curve distributions that best fit three theoretical niche models (Lognormal, Niche Preemption, and Power Law). The Lognormal distribution had the highest diversity and both the Niche Preemption and Power Law having medium to low diversity. Community metabolism did not differ between habitation, region, or geology; although 60 metabolic categories significantly differed between niche models. Communities that best fit Niche Preemption model show metabolic enrichment of stress response and efflux pathways. Whereas Power Law model communities have an enrichment of autotrophic metabolism (photosystem machinery, carbon fixation, iron acquisition, and circadian regulation). This study shows that microbial diversity is reduced by anthropogenic pressures on coral reefs, which alters community structures and selects for specific metabolic functions.