Pesticides are a major cause of reduction in the global population of amphibians. This study investigates the effect of varying concentrations of cyproconazole (1 and 10 mg/L) on Rana nigromaculata during a chronic 90 days exposure period. High levels of cyproconazole (10 mg/L) induced declined body weight, short snout-vent length, slow metamorphic development and abnormal behavioral endpoints in R. nigromaculata tadpoles. Tadpoles exposed to 10 mg/L did not survive beyond 42 days. Abnormal behaviors were observed more frequently with exposure to the highest concentration of cyproconazole. Compared with controls, the concentrations of dismutase (SOD), catalase (CAT) and glutathione (GSH) were significantly increased in tadpoles exposed to 1 mg/L cyproconazole. However, when the concentration of cyproconazole increased to 10 mg/L, concentrations of SOD, GSH and CAT activity began to decline. In addition, thyroid and gonad development were also affected at the gene and hormone level, with varied effects observed with different exposure levels and days. Exposure to cyproconazole at the lower level of 1 mg/L induced damage to histological structures of the thyroid gland. Stereoselective tissue distribution and bioaccumulation of cyproconazole was observed in tadpoles. The ranked order of bioaccumulation was: enantiomer -4 > 3> 2 > 1, with the level of cyproconazole highest in the gut. These findings reflect the toxicity of cyproconazole to R. nigromaculata and further our understanding of the effects of pesticide exposure on global amphibian population declines.