This paper provides information on the application of marker pigment analyses for estimation of phytoplankton biomass as well as qualitative and quantitative estimates of food uptake by calanoid copepods Acartia bifilosa, Giesbrecht in early summer (27 June to 2 July 1994) in the Oder estuary (Pomeranian Bight, southern Baltic sea). The marker pigment concentrations were converted into C-equivalents for comparison with data obtained by the classical Utermohl method. Both data sets were generally in good agreement, although differences were found at the taxon-specific level, which could be explained largely by limitations of the Utermohl method. The ingestion rates estimated from cell counts and marker pigment concentrations were within a comparable range (0.31 to 0.84 μgC ind.-1 d-1 and 0.50 to 1.04 μgC ind.-1 d-1 respectively), A. bifilosa showed a positive food selection for dino- and cryptophytes and an avoidance of cyanobacteria and chlorophytes. Diatoms were ingested according to their abundance. Marker pigment detection has been shown to be a useful tool for estimation of taxon-specific grazing activity in estuarine environments.