A study of the abundance and composition of microphytoplankton was carried out in marine areas of the Datça and Bozburun Peninsulas between the years 2002 and 2004. Simultaneously measured physical (salinity, temperature, secchi disc) and chemical parameters (nutrients, chl-a, dissolved oxygen) were assessed together with microphytoplankton data. Seawater and plankton net samples were taken from 63 stations during 6 sampling periods. A total of 132 taxa belonging to 3 taxonomic classes was reported and a checklist of microphytoplankton was prepared for this study area. Average nutrient values in surface water ranged from 0.01 to 1.19 µM for NO3+NO2–N, from 0.01 to 0.69 µM for PO4–P and from 0.50 to 5.31 µM for SiO2–Si and chl–a values were between 0.19 and 0.68 µg l–1 throughout the study area. The highest number of microphytoplankton cells reached 5400 cells l–1 and dinoflagellate Prorocentrum micans reached 1500 cells l–1 while diatom Thalassionema nitzschioides reached 700 cells l–1. Dinoflagellates showed a more homogeneous distribution in a wider area than diatoms. The dinoflagellate abundance increased in areas close to the fish farms due to the amount of nutrients originating there. Spatial changes in phytoplankton composition observed in this marine area revealed that phytoplankton are very sensitive to ecosystem changes. The study area could generally be defined as oligotrophic in terms of trophic status depending on the nutrient and chl–a concentrations. Moreover, very low cell abundance and high species richness observed in this area also reflect typical characteristics of oligotrophic waters.