Antarctic phytoplankton growth in winter is limited by low surface light availability due to sea ice coverage in most areas of the Antarctic, and much of the primary production is limited to sea ice algal communities. In addition, a main interannual “shift” in the chlorophyll-a size structure from diatoms to nanophytoplankton blooms during spring-summer months have been observed in the last decades. At the northern Antarctic Peninsula (nPA), seasonal sea ice extent and duration have declined significantly over the last 30 years, and these areas now often have many years with little to no sea ice, but have sunlight throughout the year. Since winter diatoms assemblages may constitute the inoculum for the spring phytoplankton bloom, studying the phytoplankton composition and their spatial variation in abundances in these sea ice/ice free regions during winter is important. We collected surface water samples (5 m) during four oceanographic cruises (AMLR – NOAA program) to the northern Antarctic Peninsula from 2013 to 2016 (July – August: austral winter). The stations were clustered in three main areas: West shelf (WS), Bransfield Strait (BS) and Elephant Island (EI). These samples were analyzed for taxa composition and abundance across a range of spatial scales and in relation to physico-chemical parameters from ice free and sea ice covered areas. Relatively high chlorophyll a, high diatom cell abundances, around EI were associated with waters of low salinity, within the Antarctic Circumpolar Current (source of Fe) during winters 2013-2016. Very low chlorophyll a and low diatom abundances in WE (offshore) and BS (inshore) stations, were associated with waters of high salinity, concurrent with the presence of El Niño conditions during 2015-2016. Higher nanophytoflagellates abundances, relative to diatoms, were observed during winter 2014, dominating the size structure of phytoplankton in all areas. Our results provide insights into the spatial variability of phytoplankton groups during austral winter, and demonstrate that regional climatic (El Niño), -cryospheric (sea-ice extension), and oceanographic (water masses) features are likely to affect the phytoplankton functional groups growth in nAP.