Marine sponges are prolific sources for new bioactive compounds and they may contain microorganisms that can comprise up to 40% of the total sponge biomass. Therefore, it is important to understand the function and the specific interactions of sponge-associated microorganisms. In this study, we assessed the composition of predominant bacterial and fungal communities using DGGE fingerprinting of Sarcotragus sp. and Petrosia ficiformis collected from the Aegean Sea. Total community DNA extracted with the indirect DNA isolation method by using collagenase followed by 16S rDNA and ITS amplification of 16S rDNA and ITS amplicons were subjected to DGGE profiling. A total of 8 and 21 individual DGGE bands from 16S rDNA-V3 and ITS1 fragments were sequenced, respectively, and matched to corresponding bacteria and fungi in the GenBank database. Methylobacterium sp. and Chalastospora gossypii from Sarcotragus sp. and Gibberella intermedia and Fusarium subglutinans from Petrosia ficiformis are reported for the first time from marine sponges. Associated microorganisms of Sarcotragus sp. and Petrosia ficiformis are considered as host-specific, as tested sponges from the same geographical location showed different dominant bacterial and fungal diversities.