Coral reefs are biodiverse ecosystems which rely on microorganisms for nutrient cycling, immune benefits, and contributing to general ecosystem function and stability. Microorganisms reside in diverse coral reef habitats including the water column, sediments, reef surfaces, and in association with reef life. This chapter focuses on the prokaryotic (Bacteria, Archaea) members of the reef community. First, a history of major discoveries and advancements about Bacteria and Archaea in reef environments is presented, alongside the significance of these findings. Then, attention to bacterial and archaeal communities residing in reef water, sediment, and select reef organisms (corals and fish) is presented. Within each habitat, there is a focus on (a) general trends in the diversity, composition, and functions of microorganisms, (b) dynamics of the microorganisms and connection to reef health and (3) outlook and future research needs. Overall, there has been considerable progress observing and inventorying Bacteria and Archaea in reef environments. Many opportunities exist to further this understanding into specific mechanisms surrounding the role of specific microorganisms and microbial communities in host and reef ecosystem biogeochemistry, health, resilience and applications of this knowledge into conservation and restoration activities.