Coral reefs are one of the most biodiverse and productive ecosystems on Earth, as evidenced by the multitude of colorful and vibrant hard and soft corals, sponges, fish, and other reef dwellers. Beyond this visually accessible biodiversity, coral reefs host a vast array of microbial communities that play crucial roles in maintaining reef health and stability. This chapter explores the immense diversity of microorganisms including bacteria, fungi, viruses, and microeukaryotes that inhabit coral reefs. It also examines how microbial communities are structured by abiotic and biotic factors, and how microbial processes contribute to ecosystem function and resilience. This chapter provides an overview of the microbial diversity within coral reefs with a focus on non-host-associated microorganisms, the factors influencing their diversity, and the processes mediated by these microbes. Furthermore, this chapter highlights the significance of microbes as indicators for evaluating reef health and supporting biodiversity monitoring. Finally, the chapter discusses the potential of microbes as agents for active interventions relevant for conservation and biodiversity monitoring.