Among the multiple forms of freshwater pelagic cyanobacteria, the phycoerythrin-rich species Planktothrix rubescens is well adapted to temperate, deep and large lakes. In Lake Geneva, this filamentous and microcystinproducing species has been the dominant cyanobacterial species observed since the early years of this century. In addition to the trophic state (e.g., the phosphorus level), the influences of air and water temperature on the occurrence and development of cyanobacteria are particularly relevant in the context of global climate change. The latter may indeed be particularly marked for lakes in the Alpine region, with a rate of warming that may be twice as large as the global average. The impact of climate change on P. rubescens is thus an important challenge and it has been analysed in this study through two different approaches: (1) the extreme air temperature events as a proxy for future climate and (2) the multi adaptive regression splines (MARS) model to predict future P. rubescens biomass. These methods allowed us to determine whether Lake Geneva will still sustain an important biomass of P. rubescens in forthcoming years, provided there is no severe over-enrichment with nutrients in the future. The outcomes strongly suggest that the fraction of cyanobacterium could increase with respect to the total phytoplankton community by as much as 34 % by the end of this century and induce a significant change in the microalgal composition. Additionally, the results point to the fact that spring is a key period during which air temperature and nutrients become the determinant factors for outbreaks of this species in the subsequent seasons.