1. The variability in the stable isotope signatures of carbon and nitrogen (delta C-13 and delta N-15) in different phytoplankton taxa was studied in one mesotrophic and three eutrophic lakes in south-west Finland. The lakes were sampled on nine to 16 occasions over 2-4 years and most of the time were dominated by cyanobacteria and diatoms. A total of 151 taxon-specific subsamples covering 18 different phytoplankton taxa could be isolated by filtration through a series of sieves and by flotation/sedimentation, followed by microscopical identification and screening for purity. 2. Substantial and systematic differences between phytoplankton taxa, seasons and lakes were observed for both delta C-13 and delta N-15. The values of delta C-13 ranged from -34.4% to -5.9% and were lowest in chrysophytes (-34.4% to -31.3%) and diatoms (-30.6% to -26.6%). Cyanobacteria were most variable (-32.4% to -5.9%), including particularly high values in the nostocalean cyanobacterium Gloeotrichia echinulata (-14.4% to -5.9%). For delta C-13, the taxon-specific amplitude of temporal changes within a lake was usually < 1-8% (< 1-4% for microalgae alone and < 1-8% for cyanobacteria alone), whereas the amplitude among taxa within a water sample was up to 31%. 3. The values of delta N-15 ranged from -2.1% to 12.8% and were high in chrysophytes, dinophytes and diatoms, but low in the nitrogen-fixing cyanobacteria Anabaena spp., Aphanizomenon spp. and G. echinulata (-2.1% to 1.6%). Chroococcalean cyanobacteria ranged from -1.4% to 8.9%. For delta N-15, the taxon-specific amplitude of temporal changes within a lake was 2-6%, (2-6% for microalgae alone and 2-4% for cyanobacteria alone) and the amplitude among taxa within a water sample was up to 11%. 4. The isotopic signatures of phytoplankton changed systematically with their physical and chemical environment, most notably with the concentrations of nutrients, but correlations were non-systematic and site-specific. 5. The substantial variability in the isotopic signatures of phytoplankton among taxa, seasons and lakes complicates the interpretation of isotopic signatures in lacustrine food webs. However, taxon-specific values and seasonal patterns showed some consistency among years and may eventually be predictable.