Use of insecticides in agriculture to increase crop yield is potentially detrimental to the ecosystem due to potential harmful effects to non-target species living in the same area. Amphibians are among the most commonly affected species by insecticides. In order to explore the effect of three widely used insecticides on amphibians, the eggs of Japanese wild frogs were exposed to Clothianidin, Chlorantraniliprole and Cartap. Then Xenopus laevis embryos were exposed to these insecticides to evaluate the underlying genetic mechanisms of insecticide-induced malformations using microarray analysis. Results indicated that Clothianidin and Chlorantraniliprole were not teratogenic to the wild frog and Xenopus embryos. Cartap was lethal to both wild frog and Xenopus embryos at concentrations above 2mg/L.  Cartap also induced four main malformations namely, hypopigmentation, bent axis, wavy notochords and fluid blebs on Xenopus and wild frog embryos. Microarray analysis was conducted using the malformed Xenopus embryos to find out Cartap-induced gene expression changes. The differentially expressed genes yielded from microarray enriched Gene Ontology terms and KEGG pathways related to biological processes such as development, cell differentiation, nucleotide metabolism, immune processes and hematopoiesis. These results demonstrate the teratogenicity of Cartap by affecting the vital biological processes.