Reef-building corals associate with a wide diversity of microorganisms, including intracellular dinoflagellate photosymbionts (Symbiodinium spp.), other protists, fungi, viruses, bacteria and archaea. Some of these microbes are known to confer benefits to their coral host through provisioning of photosynthate and enhancement of calcification (Symbiodinium), nitrogen fixation (Symbiodinium and prokaryotes), sulphur cycling (prokaryotes), and prevention of infection by pathogens (prokaryotes and viruses). Further, coral physiological traits are affected by the specific microbial symbiont taxa harboured. For instance, full-sib coral recruits inoculated with certain distinct Symbiodinium strains differ in growth rate and upper thermal tolerance. Conversely, under conditions of environmental disturbance some microorganisms can cause coral bleaching (the loss of the photosymbionts causing a paling of the coral tissues) and disease. In my plenary, I will primarily focus on our work relating to the Symbiodinium symbionts: their genetic and physiological diversity, their thermal stress responses, their interactions with and influence on the coral host animal. In addition to our work on photosymbionts, I will also present some of our research into the highly diverse viral assemblages associated with corals. Some viruses target Symbiodinium and I will demonstrate that these may be involved in the Symbiodinium thermal stress response, and by inference, coral bleaching susceptibility. Viruses also target bacterial pathogens of corals, such as the cyanobacteria that dominate the Black Band Disease microbial mat. These viral infections are recorded in the cyanobacterial CRISPR spacers, indicating and arms race is ongoing between phage and host. Finally, I will talk about the ways in which we are manipulating the Symbiodinium and prokaryote symbionts with the aim to enhance environmental stress tolerance of corals. Coral health and cover is declining rapidly across the globe due to increasing greenhouse gas concentrations in the atmosphere and other anthropogenic disturbances, and interventionist approaches such as microbiome manipulations may be required to assist coral reef ecosystems in persisting into the future.