The global climate change is known to involve in the decline of biodiversity from different ecosystems, including coral reefs worldwide. The spatial distribution of reef associated flora and fauna in the Gulf of Mannar (GoM) Marine Biosphere Reserve (GOMMBR) are declined due to damage of coral reefs by three major global problems observed in coral reefs, pertaining to frequent bleaching events, sedimentation and overwhelming algal communities. The occurrence of rich biodiversity in reef areas indicates the healthy condition of an iconic reef ecosystem. In this study, to assess the health status of coral reefs in Mandapam group of Islands under GoM, the diversity and distribution patterns of species composition assembled in reefs at seven Islands were analyzed. In 2019, summer temperature range was exceeded between 32 to 36 °C than usual range 28 to 30 °C, which resulted again massive coral bleaching in GoM. Statistical analysis revealed the high diversity of macroalgae in all the reef sites at Mandapam group Islands. Considerably, dead reefs in Mandapam group Islands represent 90% of algal communities and very less to scarce faunal diversity. While, faunal diversity was well diversified in the live coral cover areas and reefs with less macroalgal assemblage. This assessment provides current reef biodiversity data for gaining further insights into complex spatial distribution patterns of reef biota in GoM, and this will support the authorities to plan conservation efforts and to support livelihood of local fisher folk community.