Seasonal variations in autotrophic and heterotrophic picoplankton community structure were studied by flow cytometry at 3 shelf stations in the central Cantabrian Sea (southern Bay of Biscay), from April 2002 to April 2003. A marked seasonality was found for autotrophs, with cyanobacteria (Synechococcus and Prochlorococcus) being more important in nutrient-depleted waters (June to October, 75 ± 3% of picophytoplanktonic cells) whereas picoeukaryotes clearly dom- inated in terms of biomass during the rest of the year (82 ± 2%). The absence of Prochlorococcus in spring and summer seems to be related to hydrology rather than to nutrient conditions. Under strati- fication the maximum abundance of cyanobacteria was found above the nutricline, in contrast to picoeukaryotes. Autotrophic groups cell size was strongly influenced by nutrient conditions while chlorophyll a fluorescence varied in parallel to irradiance. Heterotrophic bacteria were less variable than picophytoplankton and high nucleic acid content (HNA) cells dominated the community in win- ter and spring (64 ± 1%) but only at depth during the rest of the year. A similar response of low nucleic acid content (LNA) bacteria to environmental conditions suggests they are, at least partially, metabolically active, in contrast to the commonly held view that they are a homogeneous group of dead or dormant cells. A larger mean size of LNA compared with HNA bacteria was consistently observed in winter and spring. Regardless of variations in abundance and group composition, the great constancy of the picoplanktonic contribution to integrated algal biomass (17 ± 2%) over the seasonal cycle outlines the importance of picophytoplankton also in coastal zones.