Natural populations of heterotrophic nanoflagellates were reduced in numbers and in situ growth rates during a toxic Microcystis bloom in a eutrophic lake. Microcystin was found in the particulate phase (algae) and in the dissolved phase (water) with maximum concentrations of 414 μg g freeze-dried algal material^-1 and 141 μg l^-1 lake water, respectively. An average reduction in growth rates of 49% was found when comparing the growth estimates before and after the toxic bloom had peaked. Similar reductions were found in laboratory experiments when growing mixed flagellate populations from two different systems with microcystin, but without predators. Concentrations of 10 μg toxin l^-1 reduced the growth rates by 36-41% (significantly different from the controls) and 1 μg toxin l^-1 reduced the growth rates by 24-28% (not significant). Thus, natural populations of heterotrophic nanoflagellates seem very sensitive to microcystin. The growth characteristic of two cultured species was also tested in the presence of microcystin. Both the cultured species, Heteromita globosa and Spumella sp., grew well at 1-10 μg microcystin l^-1 and Spumella sp. was able to grow at 50 μg microcystin l^-1. However, the growth curves indicate that the decline in numbers during the stationary phase occurred faster in the presence of microcystin. The ecological consequences of a highly sensitive protozoan community may be that larger zooplankton species (copepods and cladocerans) are affected by reduced availability of food.