Microcystis aeruginosa is generally dominant in many Mexican freshwater ecosystems interacting with zooplankton species. Hence, feeding and filtration rates were quantified for three cladoceran (Daphnia pulex, Moina micrura and Ceriodaphnia dubia) and three rotifer species (Brachionus calyciflorus, Brachionus rubens and Plationus patulus) using sonicated M. aeruginosa alone or mixed with Scenedesmus acutus in different proportions (25, 50 and 75%, based on cell density), offering a combined initial density of 100,000 cells·ml(-1). All the three cladoceran species ingested M. aeruginosa (100-300 cells ind(-1) min(-1)) when fed exclusively with cyanobacterium. When green alga offered as exclusive diet, the number of cells ingested by the tested cladocerans varied from 80 to 400 cells ind(-1) min(-1). Compared to cladocerans, rotifers in general consumed much lower quantity (< 200 cells ind(-1) min(-1)) of M. aeruginosa and S. acutus. The filtration rate for Daphnia pulex was inversely related to the proportion of green alga in the diet. For other tested cladocerans, no such clear trend was evident. In mixed treatments containing M. aeruginosa, the filtration rate of Daphnia was highest (about 220 μl ind(-1) min(-1)) when the medium contained 75% of S. acutus. Among the rotifer species, P. patulus filtered highest volume (100 μl ind(-1) min(-1) from mixed diets containing higher proportions (50 or 75%) of M. aeruginosa. Thus, there were species-specific differences in the filtration and feeding rates of zooplankton when offered mixed diets of green algae and toxic cyanobacteria. These probably explain the coexistence of different zooplankton species in Microcystis-dominant waterbodies.