The Andaman Islands characterize one of the relatively unexplored coral reef zones of the Indian subcontinent. A few benthic biodiversity studies have been carried out to date, but several coral and algal species still remain to be evaluated in terms of their abundance, vigour and conservation priority. In absence of a comprehensive, reliable dataset, inter-relationships between anthropogenic impacts and climate alterations with the coral reefs cannot be assessed authentically. This paper addresses the coupled themes of biodiversity and reef management in the Andaman Islands by examining the percentage cover of corals and benthic algae from shallow-water ecosystems across the coasts of Havelock, Neil, Ross, Jolly Buoy Islands and Chidiyatapu beach proximal to Port Blair. Four major reef types were observed: coral-dominated, algae-dominated, neutral setting and algae overgrowing dead reefs. Jolly Buoy Island had the highest percentage cover of scleractinian corals and crustose coralline algae. Turf algae were most abundant at the Ross Island, while other macroalgae showed highest abundance at Chidiyatapu. Overall species diversity values for corals and algae were highest at the Jolly Buoy and Chidiyatapu, respectively. Given that corals and algae are critical reef components, management paradigms must consider the abundance and frequency of both these biogenic entities in the seascape. The needs, expectations and objectives of the people dependent on coral reef ecosystems also need to be considered. Long-term monitoring is imperative in understanding the natural typology of reefs and managing the possible algal encroachments. Refined management efforts that include greater thrust on development of marine protected areas and reserves; establishment of connectivity between various coral ecosystems of the region; control of invasive algae; and increasing awareness among the local people as well as tourists will ensure continued support of ecosystem to maintain healthy reefs. Collectively, the results are used to promote some strategies to conserve the Andaman coral reefs and cope with the detrimental anthropogenic and climate changes in these coastal habitats.