The inhibitory effects of cyanobacterial compounds as possible explanation of the lack of stable Cyanobacteria–Cryptophyta coexistence in steady-state phytoplankton assemblages were studied. The possible interactions between two phytoplankton species, a toxic Microcystis aeruginosa (cyanobacteria) and a non-toxic Cryptomonas ovata (Cryptophyta) were investigated (i) in mixed cultures (containing C. ovata and M. aeruginosa cells); (ii) in M. aeruginosa crude extract-treated C. ovata cultures and (iii) in purified microcystin-LR (MC-LR) treated C. ovata cultures. The results of experiments proved that the presence of living M. aeruginosa cells have more inhibitory effects on C. ovata cultures than the crude extract of the M. aeruginosa cells; or the presence of the purified MC-LR. These results suggest that MCs does not play as important role in cyanobacteria–Cryptophyta interaction as it was presumed; hence more complex effects (allelopathy among them) can be significant in shallow lakes ecosystems.