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Phytoplankton composition, abundance and carbon biomass were investigated at monthly intervals during 2006–2007 at a coastal site, “Acqua Alta” an oceanographic tower, in the northern Adriatic Sea. Results were compared with chlorophyll a concentrations of phytoplankton classes attributed by HPLC-CHEMTAX analysis. Changes in the taxonomic structure were associated with environmental parameters. The total carbon biomass of phytoplankton was positively correlated with the temperature and negatively correlated with silicate concentrations. Nutrient concentrations were higher in the winter–spring period than in the summer-autumn period. The highest carbon biomass and abundance of phytoplankton were observed during summer–autumn months. Diatoms were the group that had the highest contribution to the total carbon biomass during the sampling period. Small flagellates, which were the major contributors to the total cell counts were dominant during the summer period. There was a significant correlation between carbon biomass and CHEMTAX-derived Chl a values of diatoms and dinoflagellates. However, the total carbon biomass of phytoplankton was not correlated with Chl a, which seemed to be related to seasonal changes in the ratios of C:Chl a of all taxonomic classes. This ratio was higher during the summer-autumn period (73 ± 33) than during the winter–spring period (17 ± 20).