In the framework of the multidisciplinary Italian project VECTOR, aimed at evaluating the carbon cycle in the pelagic systems of the Mediterranean Sea, the spatial and temporal variability of phytoplankton were investigated in the southern Adriatic Sea in the period November 2006-June 2008. Three stations were sampled along the Bari-Dubrovnik transect with a seasonal frequency (except summer 2007 and spring 2008) at four depths (surface, maximum fluorescence depth and two intermediate depths), with the aim of analyzing the structure of phytoplankton community and evaluate the standing stocks of the three size fractions (pico-, nano- and microphytoplankton). Abundances were on average 5.41 • 107 ± 5.97 • 106 cells l-1 for picophytoplankton, 1.00 • 106 ± 6.70 • 104 cells l-1 for nanophytoplankton and 2.16 • 104 ± 7.46 • 103 cells l-1 for microphytoplankton. Total biomass ranged from 8.5 to 80.7 µg C l-1. The highest values were recorded in April 2007 (38.4 ± 5.9 µg C l-1), while the lowest ones in February 2008 (13.8 ± 1.5 µg C l-1). Picophytoplankton was generally the most abundant phototrophic fraction (on average, 96% of the total abundances and 49% of the total biomass), while nano- and microphytoplankton provided a minor contribution (4 and less than 1% of total abundance and 35 and 16 % of total biomass for nanophytoplankton and microphytoplankton, respectively). A decreasing gradient from west to east was observed for pico- and nanophytoplankton abundances and for total biomass. The low biomass values and the dominance of the autotrophic picoplankton fraction in the whole area reflected a general oligotrophic condition. The easternmost station (AM9), characterized by the lowest phytoplankton abundances and biomass and low nutrient concentrations, resulted still more oligotrophic and probably influenced by the Ionian Surface Water (ISW), coming from the eastern Mediterranean.