Food selection by 2 dominant calanoid copepods, Acartia sp. and Temora longicornis, was studied during mass occurrence of N2-fixing cyanobacteria in June/July 1993 and 1994 in the Gotland Sea (Baltic Proper). The aim of this study was to assess the importance of N2-fixing cyanobacteria in the diet of calanoid copepods. Two different methods were used: firstly the analysis of marker carotenoids by HPLC (high-performance liquid chromatography), and secondly the analysis of δ15N signals of copepods by mass spectrometry. The first method provides a 'snapshot' of autotrophic material ingested; the second method summarises a longer period, and gives evidence that a certain food source is not only ingested but also assimilated. In 1994, mass occurrence of cyanobacteria showed a higher concentration in the euphotic layer than 1993 (97 pg C l-1 in 1994, 57 pg C l-1 in 1993), which was reflected in higher food uptake of N2-fixing cyanobacteria in 1994. The average relative amount of myxoxanthophyll, the specific carotenoid of N2-fixing cyanobacteria, in the copepod guts showed high values in 1994 (Acartia sp. 37%, T. longicornis 41%) and low values in 1993 (1% for both copepods). The low δ15N values of both Acartia sp. and T. longicornis in 1994 (9‰) compared to those in 1993 (10.5‰) support the results of HPLC analyses, because N2-fixing cyanobacteria have a lower δ15N (average 0.7‰) than eukaryotic phytoplankton (average 12‰). The low δ15N values in 1994 indicate that N2-fixing cyanobacteria were not only ingested but also assimilated by the copepods to a higher extent in 1994 than 1993.