The aim of this study was to test seagrass-associated fungi that have antibacterial activity against Vibrio alginolyticus and Vibrio parahaemolyticus. Seagrass sampling, fungi isolation, antibacterial screening, and molecular identification were used in this study. The antibacterial screening found that 2 out of 10 isolates were positive for antibacterial activity. This includes a seagrass-associated fungi of Thalassia hemprichii, which has green colonies. This isolate has no exudates and has a green reverse. The other isolate TA.EA.1.3 was a seagrass-associated fungi of Enhalus acoroides, white in color, with exudates and a brown reverse. The isolate extracts weighed 256 mg and 2017.9 mg, respectively. The antibacterial activity of the TA.TH.1.1 fungal isolate extract against V. alginolyticus and Vibrio parahaemolyticus was classified as strong because of the inhibition zone produced, which was 10-20 mm. The antibacterial activity of the TA.EA.1.3 isolate, classified as moderate, produced 5-10 mm of inhibition zone. Molecular identification showed that isolate TA. TH.1.1 was Aspergillus unguis (100% homology) and TA.EA.1.3 was Aspergillus versicolor (100% homology). In conclusion, A. unguis and A. versicolor have antibacterial ability against Vibrio alginolyticus and V. parahaemolyticus as antifouling bacteria.