Margosa oil (Azadirachta indica) extract as biopesticides were examined against Culex pipiens mosquito larvae under laboratory conditions to detect the toxicity of margosa oil extract and study the histopathological alterations in the midgut of treated larvae. The inhibition influence of plant extract was assessed by determining the mortality of larvae post-treatment with LC50 value11.59 ppm. The crude extract of margosa oil recorded 90% mortality for Cx. pipiens at 80 ppm. In contrast, the lowest concentration of extract recorded 30% mortality. Histological analyses showed that treated larvae had cytopathological alterations of the midgut epithelium. The treatment at high concentrations of margosa extract showed more damage in the gizzard and midgut region, leading to death. On the other hand, the treated larvae with low concentration exhibited little changes in the gizzard dendrites. The study provided that margosa oil is promising as a larvicidal agent against Cx. pipiens, naturally revolved biopesticides would be an alternative to chemical insecticides.