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Global warming has been considered to accelerate the expansion of cyanobacterial blooms, which are frequently composed of the bloom-forming genera, Microcystis and Pseudanabaena, in freshwater ecosystems worldwide. Nonetheless, the impact of changes due to toxin production or lack thereof on the growth of co-existing strains, both arising from increasing temperature, has remained unknown to date. We conducted competition experiments involving toxic Microcystis PCC7806, a non-toxic mcyB− mutant, and two strains of Pseudanabaena (TH-1 and DC-1) identified as P. mucicola. In mono-culture, the specific growth ratio of Pseudanabaena increased; nevertheless, the maximum cell density declined with increasing temperature. The maximum growth ratios of Pseudanabaena TH-1 and Pseudanabaena DC-1 were 0.512 day−1 in the 30 °C group and 0.440 day−1 in the 35 °C group, respectively. The optimum temperature for the growth of Pseudanabaena was 25 °C. Remarkably, there was no significant disparity in the maximum cell density of Microcystis PCC7806 and the mcyB− mutant across varied temperature groups, even though their maximum growth rates differed marginally, reaching 0.280 day−1 and 0.306 day−1 in the 30 °C group, respectively. In co-cultures, the growth of Pseudanabaena TH-1 was uniformly inhibited, whereas that of DC-1 was somewhat influenced by co-culturing with toxic and non-toxic Microcystis, except for the 35 °C group, where inhibition was absent amongst DC-1 and Microcystis. Moreover, the growth of Microcystis was promoted with a co-culture of TH-1 in the 20 °C groups. Conversely, the co-culture of Microcystis with Pseudanabaena DC-1 led to the inhibition of the former in the 30 °C and 35 °C groups. With a Lotka–Volterra competition model, the results showed that Microcystis dominated or co-existed with Pseudanabaena, conforming to expectations from the wild. [ABSTRACT FROM AUTHOR]