The climatology and interannual variability of winter phytoplankton was analyzed at the Long Term Ecological Research Station MareChiara (LTER-MC, Gulf of Naples, Mediterranean Sea) using data collected from 1985 to 2006. Background winter chlorophyll values (0.2–0.5 μg chl a dm⁻³) were associated with the dominance of flagellates, dinoflagellates, and coccolithophores. Winter biomass increases (<5.47 μg chl a dm⁻³) were often recorded until 2000, generally in association with low-salinity surface waters (37.3–37.9). These blooms were most often caused by colonial diatoms such as Chaetoceros spp., Thalassiosira spp., and Leptocylindrus danicus. In recent years, we observed more modest and sporadic winter biomass increases, mainly caused by small flagellates and small non-colonial diatoms. The resulting negative chl a trend over the time series was associated with positive surface salinity and negative nutrient trends. Physical and meteorological conditions apparently exert a strict control on winter blooms, hence significant changes in winter productivity can be foreseen under different climatic scenarios.