Marine fungal endophytes are an important repository of novel bioactive compounds and secondary metabolites which could be potential drug targets. Among all the marine organisms, macro algae (seaweeds) is the paramount sources of fungal endophytes. Endophytic fungi have a strong mutualistic association with their host by secreting bioactive compounds that aids the host in stress resistance and tolerance. Objectives: The present study aims at isolation of endophytic fungi from two seaweeds and to observe the antimicrobial activity of the fungal extracts. Methods: In this study, two seaweeds Haloplegma and Halymenia were collected from Mandapam coast, Ramnad district, Tamil Nadu, India. The endophytic fungi were isolated from the seaweed samples following standard procedure and the pure culture of the isolates were characterized based on the spore morphology. The crude extracts of the fungal isolates were extracted using hexane and screened for its anti-microbial activity through well-diffusion assay. Results: A total of four fungal endophytes from isolated from the two seaweeds. They were morphologically identified as Alternaria sp., Mucor sp., Cladosporium sp., and Aspergillus sp. The fungal extracts at varying concentration ranging from 100 μg-1000μg showed varying degrees of antimicrobial activity against four different pathogens viz., Penicillium sp., Aspergillus flavus, Escherichia coli, and Staphylococcus aureus. The Minimum inhibitory concentrations (MICs) were determined, that ranged from 0.1-1 mg of fungal extracts against the test pathogens. Conclusions: Our study is the first report to isolate endophytic fungi from Haloplegma duperreyyi seaweed. Our observations suggest that these fungal endophytes could be promising sources for metabolites with anti-microbial potential. Nonetheless, further detailed studies on other bioactive potentials of these fungal extracts would pave way for discovery of new antibiotics for a wide spectrum of infections.