Two marine areas (the northern Aegean Sea and southern part of the Sea of Marmara, Turkey) which have different trophic and hydrodynamic characteristics were compared regarding diversities of bacteria, phytoplankton, zooplankton, benthos, fish and cetaceans. During the study period (2006–2007), a total of 27 taxa of aerobic heterotrophic mesophilic bacteria including ten bacterial classes were reported for the first time from both seas. A total of 103 taxa from seven algal classes were determined. Copepod species in the northern Aegean Sea and southern part of the Sea of Marmara were recorded as 44 and 27, respectively. A total of 523 underwater photographs were taken at ten stations and the benthic organism diversity were examined for the first time using the photo-quadrat technique. A total of 72 fish belonging to 36 families, were determined. During the study, a total of 1548 nautical miles of survey effort were conducted for cetacean observation. Living individuals of the Stenella coeruleoalba (striped dolphin) were recorded for the first time. This study is intended to be the first detailed description of the diversity of bacteria, phytoplankton, zooplankton, benthos, fish and cetaceans and comparison of two different marine environments in order to put forth the situation of the ecosystem as it is today.