Phytoplankton cells are highly diverse according to their size, shape, absence or presence of the cell wall, structures surrounding the cell or in the cell itself as well as with having diverse pigments. According to those characteristics, cells can absorb, scatter or fluorescent the light which is the base of the bio-optical oceanography. During winter of 2015 and 2016 two research campaigns were conducted in the southern Adriatic Sea. The aim of the research was to measure hydrographic and bio-optical properties of the area and according those results to get insight into the processes of primary production. The consecutive winters substantially differed: while 2015 was characterized by deep vertical mixing, chlorophyll a signal and viable phytoplankton cells detected up to 500m depth, 2016 exhibited much weaker vertical mixing, reaching only Chl a up to 200 m depth. Intrusion was detected in the 400-600m depth layer that has never been recorded before, and indicates a change in the circulation pattern in the Adriatic Sea that may be driven by climate changes. Microphytoplankton was composed mostly of diatoms, and nanophytoplakton of coccolithophorids in both investigated years. Picophytoplankton showed community shift that is also recorded for the first time in the Adriatic Sea. Bio-optical features were following the pattern of phytoplankton distribution, showing in detail the spatial distribution of primary producers in the area, but not recognizing the taxonomical composition of the phytoplankton community.