This chapter explores the complex microbial communities associated with coral reefs, particularly those in extreme and marginal environments, including critical temperature regimes, mesophotic depths, low pH conditions, mangroves ecosystems, turbid environments and anthropogenically disturbed reefs, highlighting their crucial role in reef resilience and response to environmental stressors. Microbial associates of corals, known collectively as the coral microbiome, are integral to coral health, influencing nutrient cycling, disease resistance, and, consequently, overall ecosystem stability. Extreme coral communities, found naturally in suboptimal conditions, feature stress-tolerant microbiomes that resist disturbances and may underlie the holobiont (i.e., the coral host and its associated microbiome) resistance. Here, we detail the dynamics of these communities across different coral compartments and their response to a range of environmental “extremes”, which serve as natural laboratories for studying microbial adaptations to harsh conditions. The study of these microbiomes is critical in the context of the current climate change scenario, as they may provide key insights into mechanisms of coral resistance, as well as help identify potential microbial interventions, and novel conservation approaches to enhance coral reefs resilience in a rapidly changing world.