This study was conducted to determine fauna and flora assemblages of Holocene sequences from Gemlik Gulf (SE Marmara Sea) and to obtaine their similarities and differences between the assemblages of Gemlik and Izmit Bays. Total of 201 dark gray colored, fine to medium grained sandy clay samples were studied. In the drilled samples, 22 genera and 38 species were identified from the foraminifera characterizing the infralittoral zone. 40 genera and 58 species of foraminifera characterizing the upper circalittoral zone were identified. In addition, Black Sea originated Ammonia parasovica was found for the first time in cores taken from Gemlik Gulf. Nannofossil species characterizing the open-shallow marine environment Emiliania huxleyi, Reticulofenestra parvula, Coronosphaera spp., Syracosphaera spp., Helicosphaera spp. beside Gephyrocapsa oceanica, small Gephyrocapsa spp., Scyphosphaera porosa were obtained. A total of 27 genera and 37 species from ostracods were defined in the samples from gulf. Moreover, the quite abundant mollusc assemblage characterizing the shallow marine environment and fewer genera and species of diatoms were identified. The studied sequence is represented by NN21 Emiliania huxleyi biozone at the Holocene. Foraminifers and ostracods of the Gemlik Gulf are observed as Mediterranean-Aegean Sea originated assemblages. The mollusc shows the shallow marine community.