The diversity of the symbiotic fungi associated with two Red Sea sponges of the genus Hyrtios (H. erecta and H. erectus) was investigated. A total of 20 isolates were purified from these sponges. Using the morphological properties, 10 fungal strains were identified to the genus level from each sponge.  Strains isolated from H. erecta were identified to the species level using the Internal Transcribed Spacer ITS-rDNA sequences. Most of the identified fungal strains belong to the genera Penicillium and Aspergillus.  The antibacterial activities of organic extracts of these fungi were investigated against three pathogenic microbes including E. coli, S. aureus and C. albicans. All of the fungal extracts displayed moderate to high levels of antimicrobial activities against the three pathogens. Several fungal strains of the genera Penicillium and Aspergillus displayedstrong antibacterial activities provide potential for future investigation of these strains to identify the bioactive leads in these fungal extracts.