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DOI : 10.17693/yunusae.v17i26557.280523 Viewed : 3201 - Downloaded : 2811 In order to investigate phytoplankton dynamics, an offshore and a nearshore station which is mainly influenced from river inputs were sampled monthly for the period May 2010-October 2011 in the northeastern Mediterranean. In addition to phytoplankton pigment samples CTD casts for temperature and salinity were also made. Chlorophyll a as an indicator of phytoplankton biomass and seven other marker pigments representing different phytoplankton groups (Cyanobacteria, prochlorophytes, chrysophytes, prmnesiophytes, chlorophytes, diatoms, dinoflagellates) were measured by High Performance Liquid Chromatography (HPLC) technique. Surface chlorophyll a concentrations varied between <0.01 - 6.30 µg/l and 0.006 – 1.554 µg/l in the shallower coastal and deeper offshore stations, respectively. While the dominant components of the shelf phytoplankton were diatoms (27%) and cyanobacteria (25%), contribution of cyanobacteria (35%) and prymnesiophytes (27%) were more pronounced in the offshore waters. A slight increase in the diatoms` contribution to phytoplankton composition in offshore waters during winter and spring was observed. Similar increase in cyanobacteria was also observed in shelf waters after winter. When the contribution of major groups to phytoplankton composition is considered, we observe that prokaryotic picoplankton dominates the shelf and offshore waters during summer & autumn, whereas, eukaryotic nanoflagellates replaces large eukaryotes that dominate shelf waters during winter and spring in offshore waters in the mean time. Highly significant negative correlation was observed between large eukaryotes and salinity in the shelf station. Keywords : Pigments,Chlorophyll-a,HPLC,Mersin Bay