The present study deals with the mangrove associated endophytic fungi and their bioactivity profile. The fungal endophytes were isolated from the leaves of three mangrove species (Aegiceras corniculatum, Lumnitzera racemosa and Ceriops tagal) and identified by morphological and molecular methods (Internal Transcribed Spacer and β-tubulin (Ben A) sequencing). The isolates mainly belonged to Ascomycota (95%) and the Basidiomycota comprised only 5%. They come under 5 classes, 11 orders, 16 genera and 25 species. Under Ascomycota, four classes, viz., Sordariomycetes (44.5%), Eurotiomycetes (32.46%), Dothideomycetes (17.28%) and Saccharomycetes (1.83%) comprising 10 orders were recorded. Under Basidiomycota a single class viz., Agaricomycetes (3.93%) comprising 1 order (Agaricales) was observed. Colletotrichum (30.2%) was the dominant genus followed by Aspergillus (17.8%), Penicillium (14.1%), Phyllosticta (9.1%) etc. Penicillium citrinum was the dominant fungus (22%) in A. corniculatum; Colletotrichum siamense (31%) in L. racemosa and Aspergillus sydowii (35%) in C. tagal (Fig. 3). Among the isolates, the Colonization frequency (CF%) was maximum for Colletotrichum siamense (18%) followed by Phyllosticta capitalensis (11.6%). Penicillium citrinum was found in all the three plant species. Isolates from Ceriops tagal were found to exhibit higher antibacterial as well as hydrolytic enzyme production potential. Aspergillus montevidensis EF 30, Cladosporium oxysporum EF 316, Colletotrichum siamense EF 272, Penicillium chrysogenum EF 362, Colletotrichum fruticola EF 22, Ascotricha chartarum EF 374, Aspergillus sydowii EF 239, Talaromyces purpurogenus EF 313, Meyerozyma caribbica EF 347 and Schizophyllum commune EF 309 were segregated as potential strains for hydrolytic enzyme production. A. aculeatus EF 10, T. purpurogenus EF 313, C. oxysporum EF 316, C. fruticola EF 74, P. capitalensis EF 187, A. sydowi EF 226 and P. chrysogenum EF 363 showed notable antimicrobial property. T purprogenus EF 313 endowed with pigment (red) production has potential for application in dyeing industry. During the current study, 25 different species of endophytic fungal species could be recovered from three host mangrove plants and some of them were having high bioactive potential for possible commercial applications with respect to bioremediation and as antimicrobials in medicine and aquaculture.