Because of its high grazing potential, Daphnia magna is an ecologically important species in aquatic food webs. This is especially true in small, shallow ponds lacking fish, where grazing by D. magna may have a relatively higher impact on water clarity as compared to larger lakes. Thus, a reduction in daphnid abundance may have dramatic ecological consequences for shallow ponds. At the same time, shallow ponds in close proximity to agricultural areas likely experience higher concentrations of pesticides because of runoff, spray drift, and drain flow. In the present study, the acute and chronic physiological effects of the strobilurin fungicide azoxystrobin on three clones of D. magna originating from different Danish lakes were evaluated. Significant clonal variation in the sensitivity of D. magna toward azoxystrobin was demonstrated. One clone had a 48-h median lethal concentration (LC50) of 0.277 mg/L (95% confidence limits [CL], 0.145 and 0.427 mg/L), which is comparable to the value widely used in risk assessments (0.259 mg/L). The two remaining clones were far more sensitive, however, and had LC50s of 0.071 mg/L (95% CL, 0.034 and 0.126 mg/L) and 0.098 mg/L (95% CL, 0.066 and 0.139 mg/L), respectively. Furthermore, through respiration measurements and life-table experiments, sublethal stress was shown to exist at exposure to an ecologically relevant concentration (0.026 microg/L). Based on these results, we may expect changes in daphnid populations at azoxystrobin concentrations much lower than previously thought. Thus, ponds in the agricultural areas may experience changes in food-web structure even at very low concentrations of azoxystrobin.