Aquatic organisms are usually exposed to a mixture of pesticides instead of individual chemicals. However, risk assessment of pesticides is traditionally based on toxicity data of individual compounds. In this study, we aimed to examine the joint toxicity of two fungicides cyprodinil (CYP) and kresoxim-methyl (KRM) to zebrafish (Danio rerio) using a systematic experimental approach. Results from 96-h semi-static test indicated that the LC50 values of KRM to D. rerio at multiple life stages (embryonic, larval, juvenile and adult stages) ranged from 0.034 (0.015-0.073) to 0.61 (0.39-0.83) mg a.i. L-1, which were higher than those of CYP ranging from 1.05 (0.88-1.52) to 4.42 (3.24-6.02) mg a.i. L-1. Pesticide mixtures of CYP and KRM exhibited synergistic effect on embryonic zebrafish. The activities of carboxylesterase (CarE) and cytochrome P450 (Cyp450) were significantly altered in most of the individual and combined exposures compared with the control group. The expressions of seven genes (Mnsod, cyp17, crhr 2, crh, gnrhr 4, gnrhr 1 and hmgrb) were significantly altered upon exposure to combined pesticides compared with their individual pesticides. Collectively, these findings suggested joint effects should be considered in the risk assessment of pesticides and development of water quality criteria for the protection of aquatic environment.