Microbial transformations are key processes in marine phosphorus cycling. In this study, we investigated the contribution of phototrophic and heterotrophic groups to phosphate (Pi) uptake fluxes in the euphotic zone of the low-Pi Mediterranean Sea and estimated Pi uptake kinetic characteristics. Surface soluble reactive phosphorus (SRP) concentrations were in the range of 6–80 nmol L−1 across the transect, and the community Pi turnover times, assessed using radiolabeled orthophosphate incubations, were longer in the western basin, where the highest bulk and cellular rates were measured. Using live cell sorting, four vertical profiles of Pi uptake rates were established for heterotrophic prokaryotes (Hprok), phototrophic picoeukaryotes (Pic) and Prochlorococcus (Proc) and Synechococcus (Syn) cyanobacteria. Hprok cells contributed up to 82% of total Pi uptake fluxes in the superficial euphotic zone, through constantly high abundances (2.7–10.2 × 105 cells mL−1) but variable cellular rates (6.6 ± 9.3 amol P cell−1 h−1). Cyanobacteria achieved most of the Pi uptake (up to 62%) around the deep chlorophyll maximum depth, through high abundances (up to 1.4 × 105 Proc cells mL−1) and high cellular uptake rates (up to 40 and 402 amol P cell−1 h−1, respectively for Proc and Syn cells). At saturating concentrations, maximum cellular rates up to 132 amol P cell−1 h−1 were measured for Syn at station (St.) C, which was 5 and 60 times higher than Proc and Hprok, respectively. Pi uptake capabilities of the different groups likely contribute to their vertical distribution in the low Pi Mediterranean Sea, possibly along with other energy limitations.