Planktonic gross community production (GPP), net community production (NCP) and community respiration (CR) across the Mediterranean Sea was examined in two cruises, Thresholds 2006 and 2007, each crossing the Mediterranean from West to East to test for consistent variation along this longitudinal gradient in late spring to early summer. GPP averaged 2.4 +/- 0.4 mmol O(2) m(-3) d(-1), CR averaged 3.8 +/- 0.5 mmol O(2) m(-3) d(-1), and NCP averaged - 0.8 +/- 0.6 mmol O(2) m(-3) d(-1) across the studied sections, indicative of a tendency for a net heterotrophic metabolism in late spring to early summer, prevalent across studied sections of the Mediterranean Sea as reflected in 70% of negative NCP estimates. The median P/R ratio was 0.6, also indicating a strong prevalence of heterotrophic communities (P/R < 1) along the studied sections of the Mediterranean Sea. The communities tended to be net heterotrophic (i.e. P/R < 1) at GPP less than 2.8 mmol O(2) m(-3) d(-1). The Western Mediterranean tended to support a higher gross primary production and community respiration than the Eastern basin did, but these differences were not statistically significant (t-test, p > 0.05). The net heterotrophy of the studied sections of the Mediterranean Sea indicates that allochthonous carbon should be important to subsidise planktonic metabolism during the late spring.