The role of biofilm proteins in modulating cyprid metamorphosis is not well understood. In the present investigation this possibility was explored by disrupting biofilm proteins using commercially available protease. The influence of natural biofilm and artificial biofilms of Aeromonas salmonicida salmonicida and Bacillus brevis and their culture supernatants and exopolysaccharides obtained under different nutritional conditions was evaluated. Natural biofilm facilitated cyprid metamorphosis in Balanus amphitrite, whereas monospecies biofilms did not. The treatment of biofilms with protease resulted in a decline in metamorphosis, except in B. brevis, where although metamorphosis was negated initially, it increased with the protease concentration and observation days. As the response of cyprids to exopolysaccharides produced by A. salmonicida salmonicida was dependent on protein concentration, protease treatment resulted in a decrease in metamorphosis, whereas in case of B. brevis biofilms, protease hydrolysis products could be important in providing settlement cues. Thus, biofilm bacterial components play an important role in the cyprid metamorphosis of Balanus amphitrite.