This study investigates the use of chitosan nanoparticles (CHNPs) as an alternative method for managing late blight (LB) disease in potatoes, caused by Phytophthora infestans, which is considered to be a major disease in Egypt and worldwide. Therefore, reducing the reliance on pesticides and their associated risks. Five different concentrations of CHNPs (50, 100, 200, 300, and 400 mg/L) were tested in vitro, with 200 and 300 mg/L showing the highest inhibition (100%). These concentrations were then applied in the field, where 300 mg/L CHNPs significantly reduced disease severity (DS) in the Bellini and Jelly potato varieties, lowering DS from 40.3% and 37.3% (untreated) to 17.3% and 7.3%, respectively, compared to the control fungicide. Moreover, molecular markers (SCoT and SARP) revealed genetic changes in the treated plants, indicating that CHNPs induced new genes through interactions with the potato genome, potentially leading to point mutations. Overall, CHNPs showed promise for both managing LB and contributing to potato breeding efforts.