Resumo. Abstract: Aim To test the hypothesis that zooplankton changes the structure of phytoplankton in tropical reservoirs by reducing the biomass of algal species susceptible to herbivory. Methods We experimentally evaluated the species-specific responses of phytoplankton to zooplankton within eutrophic reservoirs with different phytoplankton community structure in northeastern of Brazil. Water samples were collected from the subsurface in coastal regions of the Apipucos and Mundaú reservoirs in January/2012 and November/2014, respectively, and transported to the laboratory. The experiments were performed in Erlenmeyer flasks (1 liter) filled with water from the sample sites and were maintained for five days in the laboratory conditions. Two treatments were maintained (1) with phytoplankton and the presence of the native zooplankton and (2) without native zooplankton. Results Zooplankton proved to be an important factor, modifying the structure of the phytoplankton community, especially in the Apipucos reservoir. In this reservoir, we observed a significant reduction of biomass in diatom Cyclotella meneghiniana, and the chlorophyte Chlamydomonas sp., and an increase in the biomass of Raphidiopsis raciborskii. In the Mundaú reservoir, we observed a significant reduction of C. meneghiniana and R. raciborskii, while cyanobacteria Microcystis aeruginosa increased their biomasses in the presence of zooplankton. Conclusions These results show the importance of the microalgae community structure in phytoplankton-zooplankton interactions for food webs in tropical environments, as well as support the role of zooplankton in fostering cyanobacterial growth and maintain algal blooms.