Callus of three apple (Malus domestica Borkh) rootstocks (Balady, MM 106, and MM 111) were subjected to different concentrations of silicon nanoparticles (Si-NPs) at 0, 10 and 100 mgl^-1 and polyethylene glycol (PEG) at 0, 50 and 100 gl^-1 to study its potential to drought tolerance. Callus fresh weight (FW) of Balady cv. was increased by 98.7% in PEG-drought stressed conditions after application of high concentration of Si-NPs. Total antioxidants (%), the activity of peroxidase and superoxide dismutase were higher in PEG stressed callus of Balady cv. compared to other cvs. Also, high concentration of free amino acids, proline, reducing sugars and free phenolics were observed in PEG-stressed callus of Balady cv. with increment at high level of Si-NPs. Anatomically, callus cells of Balady cv. were appeared asymmetrically and had lysigenous intercellular spaces under high level of Si-NPs and PEG. The maximum amplicons (14) were amplified using three primers SCoT 26, 66 and 77 was recorded in Balady cv. Application of Si-NPs changed the number of amplicons with different base pair in all apple cvs. under high level of PEG. It can recommend that, application of Si-NPs at 100 mgl^-1 will increase the tolerance of apple callus to drought, especially in Balady cv., followed by MM106 and MM111 cvs. as a proper drought tolerant rootstock.