This study was conducted in February, April and June 2009 at three stations in the southern Adriatic. Occurrence of the dinoflagellate Noctiluca scintillans and tunicates Salpa fusiformis and Salpa maxima in high abundances for the oligotrophic open sea, indicates the importance of physical forcing (vertical mixing) and inflow of nutrient-enriched Atlantic water, due to the Bimodal Oscillating System (BiOS) mechanism, into the Adriatic Sea thus creating an environment favourable for their rapid increase. This is the first time a bloom of N. scintillans has been recorded in the open southern Adriatic (OSA). High abundance of Noctiluca and salp populations in the OSA was characterized by low abundance of phytoplankton and other zooplankton, with obvious trophic implications (reduction of food availability to crustacean primary consumers). Moreover, during the S. maxima bloom in June 2009, calanoid copepods and appendicularians were almost completely absent (<1 ind. m−3).