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Shallow lakes are often affected by the increase in nutrients and global climate change, with frequent occurrences of cyanobacterial blooms. In this context, the biomanipulation of the higher trophic levels, such as zooplankton, can efficiently control these blooms. Based on this, this study aimed to verify the potential of a medium-sized cladoceran, Macrothrix spinosa, to control the phytoplankton biomass from the Apipucos reservoir, a shallow tropical hypereutrophic lake. For this, grazing experiments were carried out during different seasonal periods, which were characterized by the dominance of cyanobacteria in the dry season and of chlorophytes in the rainy season. The experiments were carried out in 250-mL Erlenmeyer flasks containing filtered water from the environment and different densities of the cladocerans: 0 (control), 100, 200 and 300 ind L-1. The results varied between the seasonal periods; however, M. spinosa reduced phytoplankton biomass mainly during the rainy season. In the dry season, M. spinosa significantly reduced the biomass of the morpho-functional groups IV and VII, while in the rainy season all groups were significantly reduced, except for group V. The cladoceran was also able to reduce the mean length of filamentous cyanobacteria with aerotopes (group III); one possible explanation for this result is that M. spinosa could cut the filaments before consuming them. In this way, the seasonal variations in the phytoplankton structure influenced the top-down control of M. spinosa in a shallow hypereutrophic lake, showing its potential to control algal blooms, especially of chlorophytes, and could be used in biomanipulation strategies in eutrophic freshwater environments.