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Koka Reservoir in Ethiopia has been severely impacted by water quality deterioration associated with harmful algal blooms. As a large proportion of the annual nutrient budget of the reservoir is believed to be of riverine origin, nutrient availability is presumably largely influenced by rainfall pattern and hydrological cycles, which are related to changes in climatic conditions such as El Nino-induced drought. The effect of El Nino-induced drought, which occurred in 2015, on the cyanobacterial community structure of Koka Reservoir was, therefore, investigated from May 28, 2015 to April 28 2016. The drought caused the failure of the main rainy season, which expectedly caused reduction in the external input of nutrients and changes in other limnological conditions of the reservoir. These changes, particularly nitrogen limitation, triggered the unusual dominance of the diazotrophic cyanobacterial genus Cylindrospermopsis over the previously persistently dominant nondiazotrophic genus, Microcystis, in the reservoir.