Effects of cyanobacterial toxins microcystin-LR and -RR on growth of five representatives of Chlorophyta (Chlamydomonas reinhardtii, Chlorella kesslerii, Pediastrum duplex, Pseudokirchneriella subcapitata, Scenedesmus quadricauda) and cyanobacterium Microcystis aeruginosa (Cyanophyta) were investigated in the concentration range 1–25,000 μg l−1 using microplate assays (evaluated after 4, 7 and 11 days). Our results demostrate different susceptibility of several planktonic organisms to microcystins. In some species (C. reinhardtii, C. kesslerii, P. duplex, M. aeruginosa), microcystin-RR induced more pronounced effects on growth than structural variant microcystin-LR. However, environmentally relevant concentrations of microcystins (1–10 μg l−1) did not cause significant growth alterations. Also, concentrations 100–5000 μg l−1 were ineffective in most tested species with the exception of P. subcapitata. Growth of P. subcapitata was strongly inhibited at concentrations of microcystin-LR or -RR ≥ 1000 μg l−1 after 4 days of exposure, whereas S. quadricauda was affected only at concentration 25,000 μg l−1. C. reinhardtii and C. kesslerii responded to both microcystins at the highest experimental concentration, but effects of microcystin-LR were weak and apparent only after 11 days of exposure, while microcystin-RR inhibited alga growth from day 4. Growth of P. duplex was also reduced at 25,000 μg l−1 of microcystin-RR from day 4, but only slightly inhibited by microcystin-LR (after 4 and 7 days of exposure). Growth of M. aeruginosa was only slightly affected by microcystin-LR (inhibition at 25,000 μg l−1 on day 7) and inhibited by microcystin-RR especially at the highest experimental concentration. Our results suggest that microcystin effects on phytoplankton are species specific and congener specific. However, microcystins are not likely to affect proliferation of planktonic photoautotrophs at environmentally occurring conditions. These findings do not support a hypothesis of possible direct allelopathic natural function of microcystins, at least as far as growth inhibition effects are concerned.