Marine mucilage is a cluster of visible organic compounds with a viscous structure and can be found in marine water. Mucilage has been previously reported in the Adriatic Sea, the Tyrrhenian Sea, the Mediterranean Sea, and the Ionian Sea. Identification of the mucilage composition is essential to determine which microbial communities are abundant and examine potential marine diseases that affect almost all organisms. For this purpose, eDNA metabarcoding offers quick, reliable, and diverse advantages. In this study, mucilage samples taken from Bandırma Bay are subjected to eDNA metabarcoding by using 16S rRNA and 18S rRNA regions (V3 and V4, respectively) to identify bacterial and eukaryotic diversity. ObiTools and SILVAngs were used for the bioinformatic analysis, and all species-level identifications were made using the NCBI GenBank database. According to the results, abundant species belonged to Polaribacter, Fusibacter, Vibrio, Formosa, Ulvibacter, and Marinifilum in bacterial communities, while species from Alexandrium, Gyrodinium, Thalassiosira, Eucarida, and Protodinium were found as eukaryotic communities populated the mucilage samples. This is the first marine mucilage metabarcoding study evaluating both bacterial and eukaryotic communities.