Overcoming microbial contaminants in fresh fruits is not merely by recognizing the level of contamination. Still, it requires another effort, such as applying a compound of natural and effective ingredients proven effective in reducing microbial contaminants and safe for health. The hexadecanoic acid used in this study was isolated from the tropical marine hydroids Aglaophenia cupressina Lamoureux. This study aimed to analyze the ability of bioactive compounds acid from the hydroid Aglaophenia cupressina Lamoureoux to inhibit the growth of fungi that cause rotten strawberry Fragaria x ananassa Dutch and mango Mangifera indica. Hexadecanoic acid was obtained by isolating it from the hydroid Aglaophenia cupressina Lamoureoux through the maceration, fractionation, and purification stages. Isolating fungi was done by using the PDA (Potato Dextrose Agar) medium to characterize macroscopically and microscopically and to test the inhibition using the diffusion method, which was incubated for 48 hours and 72 hours at the hexadecanoic acid concentrations of 15 ppm, 30 ppm, and 45 ppm. The results showed the hexadecanoic acid concentration of 45 ppm in the 72-hour incubation could inhibit the growth of two fungal isolates on strawberries, Fragaria x ananassa Dutch, i.e., Botrytis cinerea and Rhizopus stolonifer, for successive concentration, 24.00 mm and 22.75 mm. Meanwhile, the growth of Aspergillus niger, fungi from mangoes, could be inhibited by the hexadecanoic acid by 14.75 mm, 18.25 mm, and 23.50 mm, respectively, for the concentration of 15 ppm, 30 ppm, and 45 ppm with the 72-hour incubation.