The study of coral reefs have had a late beginning.  Earlier studies had accounted for only 218 species. Successive surveys made between 2008 and 2013 have reported the occurrence of 519 hard corals in India.

Among the four major reefs in India, Andaman and Nicobar Islands are rich in coral as compared to the relatively poorer Gulf of Kachchh.  The isles of Lakshadweep, similarly,  have more species than the Gulf of Mannar.  Among the deepwater (ahermatypic) corals, 227 species have been reported from the Indian Ocean region. However, deepwater corals have received little attention, and hence, we know of only 44 species in the Indian Seas.

Quantitative measures on the health of major Indian reefs (Gulf of Kachchh, Lakshadweep, Gulf of Mannar and Andaman and Nicobar) began after initiatives taken in 1998, with several capacity development programmes for coral reef health monitoring.

Today comprehensive base-line status assessment is available for all the major reefs. There are a number of studies addressing specific issues, which provide information on reef status: such as extent and impact of bleaching in 1998 on Indian reefs; reef status and restoration activities in Gulf of Mannar and Gulf of Kachchh, disease and stress-induced mortality in Indian reefs; coral community patterns in Andaman and Nicobar; post-bleaching recovery in Lakshadweep; impact of reef area loss due to earthquake in Andaman Islands; impact of tsunami on Indian reefs; post-tsunami status in Andaman and Nicobar Islands; and the latest bleaching episode in the Andaman and Nicobar Islands.

The Islands of Andaman and Nicobar were severely affected by the earthquake and consequent tsunami in 2004. Damages because of seismic related reef uplift in North Andaman and tsunami disaster in Nicobar reefs had caused reduction in live coral cover. The long-term impacts of bleaching, reef up-lift and tsunami on coral health is apparent from the declining trend in reef health of these reefs from status assessment data since 2000 and the latest report in 2016.

The status surveys so far, point to the fact that all the reefs in India are facing impacts of climate change and natural events to local activities – albeit in varying degrees. Siltation and eutrophication due to developmental activities on land and sea have been found to be as major, long-term and chronic stressors in all the four major reefs of India especially Gulf of Kachchh as well as throughout the Indian coast.

Bleaching has been identified as the major factor determining reef health in Lakshadweep reefs, with very little impact from local factors such as periodic dredging for boat passage in the lagoon. In  the Andaman and Nicobar islands, there is siltation and eutrophication at a minimal scale through deforestation, sewage discharge, terrestrial runoff and shore erosion associated with land subsidence in South Andaman. Gulf of Mannar reefs are stressed more in terms of intense local activities (besides regular bleaching events). Shore-based pollution, intensive fishing, illegal harvesting of protected resources compound the long-term impacts of bleaching, thereby resulting in loss of species, alteration in species dominance, and many algal dominated reefs.