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The relationship between phytoplankton distribution and dynamics, and the resident water masses in the Ionian Sea was investigated in the spring of 1999 by flow cytometry, HPLC, microscopy, ¹⁴C incorporation, and serial dilutions. More than 50% of total biomass was represented by ultraphytoplankton, with proportions increasing with depth (up to 80%) and eastward (up to 60%). Synechococcus sp. cyanobacteria dominated ultraphytoplankton numbers and biomass. Hydrological stability explained the relative vertical distribution of Synechococcus sp. and Prochlorococcus sp. cyanobacteria and their degree of photoacclimation. The northwestern area (“Italian Side”) was in a transition from bloom to oligotrophic conditions, reflected in high biological instability in terms of phytoplankton composition, photoacclimative properties, and photosynthetic efficiency (P/B of 11.40 mg C mg chl⁻¹ h⁻¹). The influence of the …