Identification of planktonic flagellates is challenging, and multiple species are often lumped together, limiting our understanding of their diversity and ecology. Our aim was to investigate changes in the phytoplankton community composition over the annual cycle in Roskilde Fjord, Denmark, focusing on the identification of organisms smaller than 20 µm. Weekly microscope and pigment data indicated a low contribution of diatoms and dinoflagellates and the importance of cryptophytes, euglenophytes and green algae, with high contributions of alloxanthin and chlorophyll b. Community composition using Serial Dilution Cultures (SDC) confirmed the high contribution of cryptophytes, prasinophytes and euglenophytes in the phytoplankton community. In contrast, diatoms only played a minor role. Seasonal changes were observed within cryptophytes, with Teleaulax dominance during cold months shifting to Hemiselmis in summer. Small prasinophytes and pico-eukaryotes were always present but had a low relative contribution to the total phytoplankton biomass. Cultured organisms enabled the identification of Hemiselmis cf. cryptochromatica, recorded for the first time in European waters, and an undescribed Pyramimonas species. We describe the new species as Pyramimonas octopora sp. nov., placed within Pyramimonas subg. Vestigiferae, based on morphological and molecular (SSU rDNA) data. The distinctive features of the new species are the eight irregularly rounded perforations arranged in a square box with rounded corners around the centre of the base plate of the box scales, and the complex crown scales, not observed in previously described Pyramimonas species.