The factors that control the production of microcystins (hepatotoxins) during cyanobacterial blooms, and the function of these metabolites remain largely unknown. In an attempt to provide answers to these questions, we compared the fitness of microcystin (MC)-producing and non-MC-producing Planktothrix agardhii strains under various experimental conditions. More specifically, we investigated the effects of temperature, light intensity and nitrate concentrations on several MC-producing and non-MC-producing strains in monoculture and competition experiments. In the monoculture experiments, no significant difference in cell growth rates was found for any of the environmental conditions tested. On the other hand, at the end of the competition experiments, we found that when the environmental conditions limited cell growth, MC-producing strains were clearly winning out over the non-MC-producing ones. This suggested that, under growth-limiting conditions, the benefits of producing MC outweigh the cost. Moreover, the reverse was found under non-growth-limiting conditions, suggesting that under environmental conditions that favour cyanobacterial growth, the cost of MC production must outweigh its benefits. These findings suggest that environmental factors may have an indirect effect on the MC production rate, and on the selection of MC-producing and non-MC-producing strains, via their direct impact on both the cell growth rate and the cell densities in the cultures. Several hypotheses have been advanced concerning the possible function of MCs, but none of them seems to be supported by our data.