The insecticidal resistance of mosquitoes necessitates the development of a natural, safe, and plant-based method for vector control. Unfortunately, there are no effective vaccines or particular medications available to combat malaria; therefore, mosquitoes must be targeted directly. Previous studies have shown the health benefits of Datura stramonium, but its bioactive peptides or proteins are less explored. This is the first study on D. stramonium stem protein used for mosquito larval protein. The present study aimed to identify the purified mosquito larval protein from the crude extract of D. stramonium stem. Crude protein was isolated, precipitated, dialyzed, and purified by using ion-exchange chromatography, native PAGE, and HPLC. The highest larval mortality was observed at 5.5 mg/ml of crude protein concentration. Native PAGE was used for the analysis and purification of active proteins. The single homogeneous purified larvicidal protein appeared as a single band of 30 kDa by SDS-PAGE. The novel bioactive peptide was characterized by LC-MS/ESI-MS. The homology of the peptide was searched by the Mascot search engine. The database search revealed has not shown peptide similarity with D. stramonium protein, but homology with another plant Arabidopsis thaliana protein is probable for protein phosphatases. The lethal concentration of purified protein against 3rd instar larvae of Anopheles stephensi had LC50 and LC90 values of 25 μg/ml and 40 μg/ml. It has shown new insight into larvicidal activity and can be used as a new drug against malaria and other mosquito-borne diseases.