Heterotrophic nanoflagellates and ciliates and their herbivorous and bacterivorous activity were studied in the frame of POMME project in north-east Atlantic, between 16 – 22°W and 38 – 45°N, during winter, spring and late summer – autumn, 2001. Ingestion rates of heterotrophic bacteria, Synechococccus and algae were measured by the use of fluorescently labeled preys. Additionally, a theoretical approach was used to estimate ingestion of Synechococcus and Prochlorococcus by heterotrophic nanoflagellates. Heterotrophic nanoflagellates and ciliate standing stock within the surface layer (0 – 100 m) showed a seasonal variation with maximal values in spring (866 mg C m^-2 and 637 mg C m^-2 respectively). However, the heterotrophic compartment was dominated by bacteria which represented more than 60 % of the heterotrophic biogenic carbon in the surface layer. Protozoa bacterivory was positively correlated with bacterial production and accounted for more than 70 % of it in the majority of sites where experiments were conducted. Grazing by heterotrophic nanoflagellates dominated bacterivory during our study. Ingestion of photosynthetic cells less than 10 micro-m in size was positively correlated with primary production and accounted for 2 – 94 % of it, reflecting differences in the evolution of the phytoplankton bloom and in the structure of the microbial food web, both associated to the strong mesoscale hydrodynamic variability of the study area. Heterotrophic nanoflagellates and ciliates are important in determining the fate of phytogenic carbon during spring. During autumn, when Prochlorococcus dominated phytoplankton community, the grazing activity of protozoa was not sufficient to control the fate of primary producers.