Microbial communities respond and quickly adapt to disturbance and have central roles in ecosystem function. Yet, the many roles of coral-associated microbial communities are not currently accounted for in predicting future responses of reef ecosystems. Here, we propose that a clearer understanding of coral-associated microbial diversity and its interaction with both host and environment will identify important linkages occurring between the microbial communities and macroecological change. Characterizing these links is fundamental to understanding coral reef resilience and will improve our capacity to predict ecological change.