Small photosynthetic eukaryotes are key primary producers in marine waters. In recent years, their diversity has been studied by the analysis of 18S rRNA gene sequences directly amplified and cloned from filtered natural samples. However, these clone libraries are often dominated by nonphotosynthetic organisms and few sequences from autotrophs are recovered. In the present paper, we developed a new approach based on flow cytometry. Photosynthetic pico-, nano- and phycoerythrin-containing (PE-) eukaryotes from the coastal English Channel were sorted based on their size and pigment fluorescence. 18S rRNA gene libraries were constructed from the DNA of sorted cells. We addressed methodological issues linked to the relatively low concentration of these cells. This novel approach confirmed that, in the English Channel, pico-eukaryotes are dominated by three genera Micromonas, Ostreococcus and Bathycoccus, while PE-eukaryotes are mainly cryptophytes from clade 4. It also revealed that nano-eukaryotes are dominated by haptophytes with important contributions from small diatoms and Prasinophyceae. It should be emphasized that haptophytes were nearly absent from clone libraries constructed from filtered samples, which explains why they have been overlooked in previous studies. The new strategy should be very useful to conduct similar studies on other specific populations that can be discriminated by flow cytometry (e.g. red tide organisms or uncultivated protists).