Global warming, as well as europhication are predicted to promote cyanobacterial blooms, but how tropical phytoplankton communities from different trophic state systems respond to temperature variation is less known. To further explore the effect of temperature changes and nutrient addition on phytoplankton communities and to get insight in possible resistance to these effects, we tested the hypothesis that temperature variation will have a stronger effect on cyanobacteria dominance in eutrophic water than in oligo-mesotrophic. Hereto, we conducted an experiment with phytoplankton communities from two aquatic ecosystems differing in trophic state. Water samples from a eutrophic and an oligo-mesotrophic system were collected and incubated in 25 and 30ºC. Also, treatments that received additional surplus N and P were included that served as eutrophication treatments. Temperature variation itself did not promote cyanobacteria in either water from the oligo-mesotrophic or the eutrophic system. However, nutrient enrichment of water from the eutrophic system significantly boosted cyanobacteria, and biomass increased 10 times in both 25ºC and 30ºC treatments. In contrast, eutrophication of water from the oligo-mesotrophic system did not change the relative contribution of phytoplankton groups and response ratios were much lower than those for water from the eutrophic system. Although using a very simple experimental design, the results suggest that in eutrophic systems cyanobacteria dominance can be favoured by further addition of nutrients, independently of a direct temperature effect and that more pristine environments possess some resistance against eutrophication. Since global warming is assumed to intensify eutrophication symptoms indirectly, our study underscores the importance of nutrient control.