Kayankerni reef is part of a complex of nearshore coral reefs extending from Vakarai in the north towards Kalkudah in the south. Additionally, rocky reefs with coral communities and areas of mixed rubble, sand and coral occur seaward of Kayankerni at depths of around 10-15m. Coral reefs within the MPA span the Thennadi bay and extend down along the northern reaches of the Vanderloos Bay. Kayankerni Marine Sanctuary consists of three separate coral areas; a fringing reef system around the headland of Elephant Point, a patch reef located approximately 2km from the shoreline, and a smaller nearshore fringing reef north of Elephant Point.
Coral reefs in the area are shallow with a maximum depth of around 8m, and the shallowest areas being less than 1m and exposed at low tide, particularly the reef crest of the coastal fringing reefs. The seaward margins of the reef consist of well defined spur and groove formations. Coral communities consist of a mix of massive, sub massive, encrusting, foliose, plate-like, digitate and branching coral colonies. This includes extensive areas of healthy branching and tabulate Acropora and foliose Echinopora, as well as large Porites domes exceeding 5m in diameter. The fringing reef lagoon and nearshore areas consist of isolated coral colonies, coral rock, algal mats, and seagrass meadows. Mangroves and lagoon habitats are found within the Elephant Point headland.
The biodiversity of Kayankerni Marine Sanctuary is yet to be fully assessed and existing species lists only represent a small percentage of the actual species found in the area. Currently, more than 50 species of hard corals have been recorded around Kayankerni with the most common species being Acropora formosa, A. yongei, Echinopora lamellosa, Favia spp., Favites spp., Montipora aequituberculata, Pocillopora damicornis, P. verrucosa, Porites lutea, P. solida, P. rus. There are also several species of soft corals belonging to the genera Sinularia, Sarcophyton, and Lobophytum. A total of 246 species of reef fish have also been recorded including 18 species of butterflyfish. The most commonly seen reef fish include snappers, fusiliers, sweetlips, parrotfish, surgeonfish, damselfish, butterflyfish, angelfish, gobies and wrasses. Common butterflyfish include Chaetodon auriga, Chaetodon decussatus, Chaetodon meyeri, Chaetodon trifascialis, Chaetodon trifasciatus, Chaetodon vagabundus, and Heniochus acuminatus. Frequently seen invertebrates include sea cucumbers, sea stars, sea urchins, sponges, feather stars, nudibranchs, molluscs, lobsters, shrimps, and anemones. Seagrass habitats contain 5 species of seagrass with the most common being Cymodocea serrulata.