The South Adriatic is a key area for the Adriatic and the deep Eastern Mediterranean mainly because it is a dense water source and a driving engine of the Eastern Mediterranean deep circulation cell. In addition, the South Adriatic is an entry point for water masses in the Adriatic. It is the place where Ionian saltier and warmer waters are mixing with Adriatic fresher waters through the process of open-ocean winter convection. The biodiversity and seasonality of bacterial picoplankton before, during and after deep winter convection in the oligotrophic South Adriatic waters were assessed combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the euphotic zone in spring when the maximum value of chlorophyll a was recorded in response to deep winter convection. The communities were dominated by Bacteria while Archaea were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values in the winter convection and spring post-convection period, and maximum values during summer stratified conditions. SAR11 was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode. Cyanobacteria were the second most abundant group strongly depending on the convection event when minimal cyanobacterial abundance was observed. Euphotic zone in spring and autumn were characterized by Bacteroidetes and Gammaproteobacteria. The Bacteroidetes clades NS2b, NS4 and NS5 and the gammaproteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. SAR324, SAR202 and SAR406 were present in the deep layer exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are strongly impacted by strong winter convection.