There is an increasing need for new tools and approaches to effectively manage the aquaculture diseases that are being considered a serious threat to sustainability. To overcome the difficulties and limitations associated with the developing resistance of microorganisms to commercial antibiotics, the discovery of new antimicrobial agents has received considerable attention, both human and veterinary medicine, from the pharmaceutical and biotechnological communities. Extracts of marine derived fungi isolated from sponges which were collected from the coast of Turkey, were screened for the antimicrobial activity against the fish pathogenic bacteria. A total of 61 fungal strains were isolated from the sponges and their ethyl acetate extracts were tested for their antibacterial activity against three fish pathogenic bacteria of Lactococcus garvieae, Vibrio anguillarum 01 and Yersinia ruckeri. According to the disc diffusion assay, 14 fungal isolates exhibited the antibacterial activity against L. garvieae, 4 isolates had antibacterial activity against Y. ruckeri and 13 isolates inhibited the growth of V. anguillarum. The two isolates of fungi were found to be able to produce broad-spectrum antimicrobial metabolites as they had strong activity against all the test pathogens. Six fungal strains had strong activity against at least one of the test pathogens. The most active strain was Penicillium atrovenetum which showed the strongest activity against L. garvieae. The screening results confirmed the possible use of sponge associated fungi as a source of antimicrobial compounds for use in aquaculture against fish pathogens.