Marine photosynthetic picoeukaryotes or PPEs, single-celled algae from 0.8 to 3 μm in size, are major contributors to phytoplankton biomass and primary production in marine systems and form diverse communities dominated by prymnesiophytes, chlorophytes, pelagophytes, and chrysophytes. Due to their ecological relevance it is important to characterize PPE community structure over temporal and spatial scales and to identify the environmental factors shaping community assembly. In this thesis we focused on major PPE groups, with the aim of determining their abundances and distribution at different spatial scales. We first characterized the fine vertical distribution of chlorophytes, pelagophytes and prymnesiophytes within the DCM (Deep Chlorophyll Maximum) developing during summer stratification in temperate areas. The distribution of these three groups, together with that of cyanobacteria, diatoms and dinoflagellates, revealed a vertical segregation of major phytoplankton groups within the DCM layer. The global ocean as sampled in the circumnavigation expeditions Malaspina and Tara-Oceans was our second scale of study, and under this context we studied the distribution patterns and abundance of a particular symbiosis between a prymnesiophyte algae and the unicellular N-fixing cyanobacteria UCYN-A, which resulted to be widespread in the global ocean. The same global approach, also including European coastal sites, provided a reliable picture of the distribution of the different pelagophyte genera and species, highlighting their low global diversity. Overall, this thesis offers new insights into the distribution patterns of different PPE taxa and provides the basis for further investigating their ecological traits