The yellow fever mosquito, Aedes aegypti, is a vector for transmitting dengue fever and yellow fever. An assessment was made of the histopathological and molecular effects of pellitorine, an isobutylamide alkaloid, on third instar Ae. aegypti larvae. At 5 mg/L concentration of pellitorine, whole body of the treated larvae became dark in color, particularly damaged thorax and abdominal regions. Pellitorine targeted mainly on midgut epithelium and anal gills, indicating variably dramatic degenerative responses of the midgut through a sequential epithelial disorganization. The anterior and posterior midgut was entirely necrosed, bearing only gut lumen residues inside the peritrophic membranes. Pellitorine caused comprehensive damage of anal gill cells and branches of tracheole and the debris was found in hemolymph of anal gills. RT-PCR analysis indicates that the compound inhibited gene expression encoding V-type H+-ATPase and aquaporine 4 after treatment with 2.21 mg/L pellitorine. The results provide a fact that pellitorine merits further study as a potential larvicide with a specific target site or a lead molecule for the control of mosquito populations.