Cyprodinil and pyraclostrobin are widely used pesticides to protect many plants from attack of microorganisms and fungal diseases. Although cyprodinil and pyraclostrobin exist in the aquatic environment at low concentration, their leftovers in the ecosystems lead to oxidative damage and interfere development in aquatic animals at environmental-relevant concentration. To figure out the combined effect of cyprodinil and pyraclostrobin, mortality and morphology were investigated in zebrafish embryos exposed to 0.1 and 1μM of cyprodinil, pyraclostobin, and their mixture. Also, gene expression profiles were investigated following exposure to both the compounds and their mixture. Mortality and morphology data showed that the mixture is extremely toxic to zebrafish embryos as it increased mortality in concentration-dependent manner and interfered development of zebrafish embryos at 72 hpf. For gene expression analysis, 0.01μM of cyprodinil, pyraclostobin, and their mixture were used. A total of 47 genes were analyzed. Genes involved in apoptosis, cell cycle arrest, DNA damage repair, drug metabolism, stress response, immune response, and lipid metabolism and transport were analyzed. Upregulation of bax for pyraclostrobin suggests that this chemical could induce mitochondrial apoptotic pathway in zebrafish embryos at 144 hpf. Upregulation of cyp1a for cyprodinil indicates that it could produce ROS and cause oxidative damage in zebrafish embryos. Altered expression of several genes for mix suggests that the mixture of cyprodinil and pyraclostrobin have inhibitory effect on gene expression. Overall, the present study suggests that the mixture of cyprodinil and pyraclostrobin could delay of zebrafish embryonic development, increase mortality of zebrafish embryos, and regulate the expression of several genes.