Mangrove ecosystems are vital coastal habitats necessary for the health and balance of marine environments. These unique ecosystems are characterized by their salt-tolerant tree species and intricate root systems, which provide essential services such as coastal protection, carbon sequestration, and nursery habitats for various marine organisms. Mangroves are known for their ability to thrive in harsh conditions, including high salinity, waterlogged soils, and fluctuating water levels, making them critical to coastal resilience in the face of climate change and human activity. Beyond their structural and ecological importance, mangrove ecosystems are home to a diverse array of microorganisms that contribute significantly to their health and functioning. They include bacteria, archaea, fungi, microalgae, and other protists, which are involved in organic matter decomposition, nutrient cycling, and sediment stabilization. They also form complex symbiotic relationships with mangrove plants. The interactions between mangroves and their associated microbial communities are intricate and help in various processes, such as enhancing the nutrient uptake of mangrove trees, assisting in detoxification processes, and contributing to the biogeochemical cycling of key elements such as nitrogen, phosphorus, and sulfur. Thus, they play a vital role in modulating the ecosystem’s ability to adapt and mitigate several environmental stressors. Furthermore, the microbial communities in mangrove sediments are pivotal for the production of several bioactive compounds of industrial and medical significance. Yet, the information regarding the microbial communities, their players, and their role remains elusive. This review aims to summarize the available information about the mangrove microbiota and its role in the mangrove ecosystem for bioprospecting.