Here we assessed the subsurface ultraphytoplanktonic (< 10 μm) community along a North-South round-trip Mediterranean transect as part of a MERITE-HIPPOCAMPE cruise campaign in April–May 2019. Temperature, salinity, and nutrient concentrations in subsurface waters (2–5 m depth) were also measured along the transect. The subsurface ultraphytoplankton community structure was resolved with a spatial resolution of few kilometers and temporal resolution of 30-min intervals using automated pulse shape recording flow cytometry. The subsurface waters were clustered into seven areas based on temperature and salinity characteristics. Synechococcus were by far the most abundant group in all prospected zones, and nanoeukaryotes were the main biomass component, representing up to 51 % of ultraphytoplanktonic carbon biomass. Apparent net primary productivity (NPP) followed a decreasing gradient along the transect from north to south and was mostly sustained by Synechococcus in all zones. These findings are likely to have implications in terms of the trophic transfer of contaminants in planktonic food webs, as they highlight the potential role of nanoplankton in contaminants bioaccumulation processes and the potential role of Synechococcus in a likely transfer via grazing activities.