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The Agatti Island is at a distance of 459 km from Kochi is located to the west of Kavaratti Island. It lies between 10º 48′ and 10º 53′ N latitude and 72º 09′ and 7º 13′ E longitude, having an area of 3.84 sq. km, with a maximum length of 10 km and width of 10km. It has a north-east, south-west trend with a long tail on the south. Agatti Island is rich for its microbial diversity especially fungi. Out of 100 different fungal organisms isolated from the deep-sea sediment of Agatti Island, 80% of the major dominated species belonged to the genus Aspergillus. Further studies of molecular characterization helped us to understand the diversity up to their species level. An attempt was made to isolate such a diverse fungi which makes an extraordinarily contribution in managing disease in humans and other animals. The deep-sea fungi that inhabit the sediment at depths of over 800 m to 1000m below the surface, have become an important source of various compounds (industrial, pharmaceutical and agricultural) based on their diversity. Reports say that there are more than 180 bioactive secondary metabolites derived from deep-sea fungi and include compounds with antimicrobial, antihelminthic, anti-cancerous, and antiviral activities. Such bioactive compounds produced by these deep-sea fungi have the potential treatments for human diseases. A halotolerant fungus Aspergillus isolated from a depth of 1429m at the Agatti was found to have antimicrobial and anticancer activity. Based on the internal transcribed spacer, 18S rRNA, and additional β tubulin and calmodulin sequencing the isolate was identified as Aspergillus terreus. Optimized production of secondary metabolites (SM) was determined at 7.0 pH, 30ºC temperature, and 10% salinity, sucrose as carbon and tyrosine and ammonium sulfate as the nitrogen source.