During a cruise in the Weddell-Scotia Confluence area (EPOS Leg 2: November–January 1988/1989) nanophytoplankton composition was determined by employing taxon-specific pigment measurements with HPLC. The biomass of the most important components was estimated by using specific pigment ratios measured in cultures of two cryptomonads and a prasinophyte. Highest cryptophyte biomass was found along the retreating ice-edge; the contribution of cryptophytes to total phytoplankton crop increased with time, reaching monospecific bloom conditions at the end of the cruise. Chlorophyll b-containing organisms and Prymnesiophyceae were present everywhere and dominated in the ice-covered part of the survey area. Cryptophyte-specific pigment measurements were in reasonable agreement with cryptophyte cell numbers. Prasinophyte cell counts, however, did not match with measured chlorophyll b concentrations. The quantitative importance of the nanophytoplankton groups reported here underlines the diversity of the plankton in the Southern Ocean's marginal ice zone system which may have implications for food chain dynamics.