Effects of prolonged darkness on Arctic phytoplankton composition were investigated with lab experiments and a pigment time series in Kongsfjorden, Spitsbergen (78°55′N). Chlorophyll a (Chl a), pigment composition, particulate organic carbon, cell numbers, and photosynthetic characteristics were studied in Arctic diatoms (Thalassiosira antarctica, Thalassiosira nordenskioeldii) and flagellates (Rhodomonas sp., Micromonas sp.) during 8 weeks of darkness and subsequent recovery in irradiance. Loss of photosynthetic functionality after 2 weeks of darkness was reversible in all species when returned to irradiance. Diatoms were more resistant to prolonged darkness (> 2 weeks) compared to the flagellates, with lower decline rates of Chl a and maximum quantum yield of PSII. T. nordenskioeldii showed rapid growth during recovery throughout 8 weeks of dark incubation, whereas recovery of flagellates diminished within 4 weeks. Ratios of taxonomic marker pigments relative to Chl a of all species showed limited variation during 8 weeks of dark incubation. The experimentally observed enhanced dark survival of diatoms was in agreement with pigment observations during four polar nights (2013–2017) in Kongsfjorden, which showed increased relative diatom abundance during declining biomass (down to 0.02 mg Chl a m−3). Therefore, a period of prolonged darkness gives Arctic diatoms a head start during the early stages of the spring bloom. The taxon-specific survival traits can influence the geographical distribution of diatoms and flagellates within the polar oceans and their phenology. Furthermore, the persistence of Chl a of nonviable phytoplankton during darkness might influence biomass estimates during the polar night.