To elucidate the changes in the proportions of microcystin (MC)-producing Microcystis, non-MC-producing Microcystis and Anabaena strains during cyanobacteria blooms, we compared their fitness under different initial biomass ratios. Culture experiments were carried out with three cyanobacterial strains: single-celled toxic Microcystis aeruginosa PCC7806 (Ma7806), single-celled nontoxic Microcystis wesenbergii FACHB-929 (Mw929) and filamentous Anabaena PCC7120 (An7120). Growth curves expressed as biovolume, Ma7806 microcystin-LR (MC-LR) content (detected with HPLC and ELISA), and the culture medium dissolved total nitrogen and dissolved total phosphorous (DTP) were measured to monitor nutrient uptake. Results suggest that the dominant strain in competition experiments between Ma7806 and An7120 was mainly controlled by the initial biomass ratio of the two strains, but there was also evidence for allelopathic interactions, where MC-LR produced by Ma7806 played an important role in the competition process. However, Mw929 was always less competitive when co-cultured with An7120 regardless of initial biomass ratio. Culture medium DTP showed significant differences between competition experiments in all sets, suggesting that Mw929 could be more suited to low phosphorus environments than Ma7806 and An7120. Overall, the competitive ability of Ma7806 was stronger than Mw929 when co-cultured with An7120 in the case of excess nutrients and the results could well unravel the seasonal succession process of cyanobacteria blooms.