Marine microbiomes associated with coral reef benthic macroorganisms, such as sponges, corals and macroalgae, play crucial roles in maintaining the health and functioning of marine ecosystems. These microbial communities form symbiotic relationships with their hosts, aiding in nutrient cycling, defense against pathogens and the breakdown of organic matter. They also contribute to crucial biogeochemical processes including nitrogen and carbon cycling, that are essential for ocean productivity. Investigating these microbiomes is critical for unlocking their biotechnological potential, including the discovery of novel bioactive compounds with medicinal and industrial applications. This chapter covers research related to microbiomes associated with benthic marine macroorganisms found at coral reefs within highly urbanized and sedimented coastal waters in Singapore. We focus on the diversity and ecological functions of symbiotic microbes associated with benthic organisms, such as scleractinian corals, sponges and macroalgae. In addition, marine microbiome research conducted on Singapore’s hard corals, sponges, nudibranchs, macroalgae and seagrasses is reviewed. Furthermore, results from our ongoing research on the exploitation of selected sponge and soft coral-associated microbes as potential sources of unique specialized molecules as anti-infectives are presented. Recent experimental data on the use of symbiotic microbes obtained from relatively resilient hard corals to confer resilience in susceptible hard corals will also be discussed. We conclude with perspectives and recommendations on future research in coastal marine microbiomes in Singapore.