Arctic ecosystems are strongly seasonal by nature, and photosynthetic organisms in particular so. In this study, the seasonality of one of the most commonly found marine photosynthetic picoeukaryotes, Micromonas pusilla, was investigated in Billefjorden, Svalbard by real-time quantitative polymerase chain reaction (qPCR). In addition, the relative abundance of pico- vs. larger-sized phytoplankton was studied throughout the spring and summer of 2011. The arctic sill fjord Billefjorden on the western coast of Spitsbergen is annually covered by fast ice and is dominated by cold, locally produced water throughout the year. Seawater samples from five depths was collected monthly from April to August, and the abundance of M.pusilla (via qPCR), the fractionated chl a biomass (cells < 3 µm vs. larger cells), and the amount of nutrients were analysed. In addition, CTD profiles and phytoplankton net hauls (20 µm mesh size) were collected at every sampling date. The Billefjorden pelagic system was in 2011 characterized by advection of warmer sea water from outside the sill in early May, and a Phaeosystis-dominated bloom that peaked in mid-May. The phytoplanktonic community had a high abundance of cells >3 µm during the peak of the spring bloom, and a picoplanktonic dominance of the chl a biomass in post bloom and late summer. Micromonas pusilla was found to be abundant below the chl a maximum in the post bloom situation in June and July, with cell numbers exceeding 6.5 x 105 cells/mL, but unidentified picoplankton dominated the phytoplanktonic community at the chl a maximum depth in June and August. During the Phaeocystis-dominated bloom in mid-May, the M. pusilla cell numbers were considerably lower and the species contributed minimally to the phytoplankton biomass.