Marine fungi are widely recognized for producing bioactive compounds with diverse pharmaceutical applications. The study aimed to investigate the antibacterial and cytotoxic properties of methanolic extracts from endophytic fungi derived from Gracilaria salicornia and Chondrus sp., collected from Argani Beach, Bali, Indonesia. Fungal isolation yielded one and three fungal strains from each host, respectively. They were later identified as Aspergillus unguis A4-1-1, Trichoderma yunnanense A5-1-1, Trichoderma asperellum A5-1-2, and Clonostachys pseudostriata A5-2-1 through ITS or LSU region comparison. Each methanolic extract underwent testing for phytochemical content, antibacterial activities, and cytotoxic potentials. Phytochemical screening indicated the presence of alkaloids in all extracts. Notably, the extract of the non-salt-treated fungus A. unguis A4-1-1 demonstrated the most potent activity with MIC values of 15.6 μg/mL against Staphylococcus aureus and Bacillus cereus ATCC 11778, while other extracts showed no substantial activity. Additionally, the salt-treated T. asperellum A5-1-2 exhibited the most potent toxic activity compared to the others with LC50 of 104.9 μg/mL, according to the brine shrimp lethality test. Other extracts showed LC50 values starting from 107.0 to 792.9 μg/mL. Given their notable antibacterial and cytotoxic potentials, it is noteworthy to identify and characterize the bioactive compounds from these fungal strains in future study.