Coral reefs or ‘the rainforest of the sea’ is considered to be the most assorted and diversified aquatic ecosystem on earth. The reef offers a varied array of benefits and applications. Despite the fact that the coral reefs are responsible for supporting millions of flora and fauna, they are under high risk of endangerment. The gradual rise in natural or anthropological activities has directed toward the deterioration and degeneration in the overall health of the coral reefs. This ultimately disturbs the productivity and sustainability of the reef ecology bionetwork and therefore led to an increase in the research interest, to study and understand the ecology and biology of the coral reefs and its associated flora and fauna. Much research has progressed and evolved over the decades in thorough understanding of the reef microbiome. In this context, the role of dinoflagellate has been well studied when compared to the other microorganisms associated with the corals. This is mostly due to the complexity associated with the reefs such as uncultivable organisms, lack of proper techniques, etc., to name a few, thereby making it difficult for proper scientific studies to be conducted. Coral-associated microbiomes act as catalysts and indicators of any kind of reef ecosystem instabilities. Such environmental stresses result in coral bleaching or any other coral-associated diseases. In consequence, understanding the microbiology of the coral hologenome may help in preventing further destruction of the coral reefs. The current book chapter aims to review the abundance, diversity and importance of the coral reef microbiome and its role in marine ecosystem sustainability. © Springer Nature Singapore Pte Ltd. 2019.