Due to the increasing constraints on using the radioactive isotope 14C to measure primary productivity (14C-PP), we determined the surface carbon fixation rates in the Mediterranean Sea, using the alternative stable isotope 13C method (13C-PP). Rates obtained (13C-POCp) were compared with simultaneous 14C-POCp measurements in samples of different volumes (72 mL and 1.2 L). We also tested the variation of the percentage of dissolved primary production (PER), to the total productivity using organic and inorganic filters (14C method). 13C-POCp rates ranged from 0.4, in the Ionian basin, to 1.5 mgC m-3 h-1 in the Ligurian region. These results agreed with those found with the 14C-PP in 1.2-L samples (two sample t-test, t = 1.035, df = 22, P = 0.31). However, we found that 14C-POCp rates derived from 72-mL incubations were 46% lower than those measured with 13C-PP. The discrepancy between large and small volume incubations was likely due to differences in the number of large phytoplankton cells within the community. PER values measured with silver membrane filters yielded similar results than those obtained using polycarbonate filters. Our findings showed that when the sample size is carefully chosen, the 13C-PP provide comparable results to 14C-PP even in waters of low productivity in the Mediterranean Sea.