In this study, we applied various developmental stages of zebrafish to address the potential environmental risk and aquatic toxicity of bromothalonil and flutolanil. This results demonstrated that the acute toxicity of bromothalonil to the three phases of zebrafish were 4.34 (embryo)<3.27 (12h old larvae)<2.52mg/L (adult fish) and that of flutolanil were 5.47 (embryo)<4.09 (72h old larvae)<3.91 (12h old larvae)<2.70mg/L (adult). Sublethal effects induced by both bromothalonil and flutolanil on zebrafish embryos were noted, including growth inhibition, abnormal spontaneous movement, slower heart rate, complete hatching failure, and morphological deformities. In addition, both bromothalonil and flutolanil could cause notochord deformation and short body length of larvae. This study provides a foundation for future investigation into the mechanism of bromothalonil and flutolanil toxicity in zebrafish.