The multi-disciplinary oceanographic cruise OBAMA_2011 was carried out in the Southern Adriatic, Otranto Strait and in the cold-water coral province of S. Maria di Leuca to investigate environmental and ecological variations occurred in the deep ocean ecosystems connected to recent climate changes. The cruise was part of the experimental phase of two research projects: EC_HERMIONE (Hotspot Ecosystem Research and Mans Impact on European Seas) and PRIN_OBAMA (Offshore OBservatory for the long-term ecological research (L-TER) on the biodiversity And ecosystem Functioning of the deep Mediterranean SeA). The main operations carried out on the cruise were: a) Recovery, servicing and redeployment of 2 instrumented moorings in the South Adriatic Sea; b) CTD profiles along transects normal to the continental slope following the pathway of the North Adriatic Dense Water (NadDW) spreading in the Southern Adriatic Sea. Water was also collected to define the spatial distribution of microzoo-, microphyto-, nano- and picoplankton populations; c) Dilution experiments to assess deep sea microbial food web functioning; d) Sediment box coring. Once onboard, each box core was subsampled for macrobenthos, meiofauna, bacteria/viruses, organic matter, enzymes, and grain size. Short sediment cores were additionally sub-sampled to measure dissolved oxygen microprofiles and to characterise the organic matter. e) Surface sediment sampling by grab in the Bari canyon. f) Acquisition of Multibeam and CHIRP sonar lines; g) Deployments of MEMO in the white coral province of Santa Maria di Leuca for observing the benthopelagic megafauna in coral and non-coral areas, and monitoring hydrographic characteristics of the bottom water; h) Outreach activity through a science journalist on board.