A field experimentwasheldduringtheseasons2019/2020 and 2020/2021 in the Regional Center for Conservation and Maintenance of Endangered Plant Genetic Resources at El-Hammam city, Matrouh Governorate, Egypt. This research was conducted on wild milk thistle (Silybum marianum var. albiflorum) cultivated and subjected to two precursors (phenylalanine and p-coumaric acid at 40 mg/L) and Chitosan nanoparticles treatments (Chs NPs 50 mg/L, Chs NPs 50 mg/L conjugated with phenylalanine 40 mg/L, Chs NPs 50 mg/L conjugated with p-coumaric acid 40 mg/L, Chs NPs 200 mg/L, Chs NPs 200 mg/L conjugated with phenylalanine 40 mg/L, and Chs NPs 200 mg/L conjugated with p-coumaric 40 mg/L) compared with the control (without the previous treatments). The study aimed to determine the effect of treatments on growth, yield, some biochemical and molecular markers. The DLS, zeta potential and X-ray diffraction were assigned for several fabricated Chs NPs. The significant highest increments in dry weight/plant, seeds weight/plant and seeds yield/feddan were obtained by phenylalanine 40 mg/L followed by Chs NPs 200 mg/L. Best biochemical markers were towards the same treatment. In the molecular level, there are no noticeable polymorphic changes in the plant genomic material with polymorphism average 59.83% for all treatments. The highest increases of total silymarin content in the plant seeds were detected by Chs NPs 200 mg/L, followed by phenylalanine 40 mg/L treatments. Concerning quantity and quality estimates, application of plants with engineered Chs nanoparticles 200 mg/L, which also has the maximum antioxidant capacity and lowest toxic product malondialdehyde at the vegetative growth period to have the highest specifications and profit is recommended.