Abstract. The seasonal and year-to-year variability of the spatial distribution of the Phytoplankton Size Classes (PSCs) has been examined in the Mediterranean Sea using the entire time series of Sea-viewing Wide Field-of-view Sensor (SeaWiFS) space observations (1998 to 2010). PSCs daily maps have been determined using an empirical model based on a synoptic relationship between surface chlorophyll a and diagnostic pigments referred to different taxonomic groups. The validation of model PSCs estimates using a Mediterranean HPLC pigments dataset revealed that the model is able to correctly detect the contribution of pico-, nano- and micro-phytoplankton to TChl a. The analysis of micro-, nano- and pico-phytoplankton satellite time series (1998–2010) describes quantitatively the seasonal and inter-annual variability of the spatial distribution of the algal assemblage structure over the basin. The analysis reveals that in most of the Mediterranean Sea the main contribution to the chlorophyll a all around the year comes from the pico-phytoplankton component, above all in poor nutrient conditions. Regions with different and peculiar features are the northwestern Mediterranean Sea, the Alborán Sea and several coastal areas, such as the north Adriatic Sea. In these areas, local interactions between physical and biological components modulate the competition between the three phytoplankton size classes. It results that, during the spring bloom season, micro-phytoplankton dominates in areas of intense vertical winter mixing and deep/intermediate water formation; while, in coastal areas, micro-phytoplankton dominates in all seasons, thanks to the nutrients supply that comes from the terrestrial inputs. In the Alborán Sea, in which the Atlantic inflow modulates the nutrient availability, any predominance of one class over the other two has been observed. Nano-phytoplankton component instead remains widespread over the entire basin along the year, and its contribution to the TChl a is of the order of 30–50%. The inter-annual variability is observed in the whole basin, but the largest inter-annual signal occurs in the northwestern Mediterranean Sea, driven by the year-to-year variation in intensity and extension of the spring bloom. In absence of sufficient in situ data of community composition, the satellite-based analysis demonstrated that pico, nano and micro classes often coexist. The predominance of one group over the other ones is strongly dependent on the physical-biological processes occurring at mesoscale. These processes directly influence the nutrient and light availability, which are the principal forcing for the algae growth.