The microdiversity and composition of culturable heterotrophic aerobic bacteria were investigated in seawater samples taken from the Sea of Marmara (an important basin between the Mediterranean and the Black Sea) in different time periods throughout 2002 2010. The bacterial isolates were identified with the automated microidentification system VITEK 2 Compact 30 (bioMerieux, France). The compositions of identified bacteria according to their exposure to environmental factors in the areas from which they were isolated were compared. The primary hydrographic parameters (temperature, salinity, and dissolved oxygen) were recorded at the sampling station. The highest heterotrophic aerobic bacteria abundance was found in the coastal stations. It was possible to isolate enteric bacteria species from the lower and upper stratification of various marine localities, which possessed salinity values between 24.0 psu and 39.2 psu during the study. Six bacterial classes were determined: Gammaproteobacteria (49%), Bacilli (34%), Alphaproteobacteria (9.09%), Betaproteobacteria (3.03%), Flavobacteria (3.03%), and Actinobacteria (3.03%). This study increases the knowledge of the composition and biochemical response of bacteria isolated from eutrophic and oligotrophic areas. Twenty-three bacteria species belonging to 16 families are reported in this study as the first records for the Sea of Marmara.