Seagrass habitats are important ecosystems due to the rich diversity of life they support, though there are few faunal inventories made in India of these areas. The Gulf of Mannar is a large shallow bay forming part of the Laccadive Sea in the Indian Ocean, wedged between the southeastern tip of India and the west coast of Sri Lanka. It is divided from Palk Bay by Palk Strait. Palk Bay in turn connects to the Bay of Bengal. These two areas have extensive seagrasbeds, coral reefs and mangrove forests. This study assessed the overall faunal diversity in this region, which will be useful in ecosystem evaluation studies.