In this study, differences in peroxidase (POD) genes of cherry root stocks resistant to NaCl (0, 50, 100 and 150 mM), and boron (0, 1.5 and 3 mM) toxicity under in vitro conditions were investigated for 3 different cherry rootstocks [Cold (Prunus avium x Prunus pseudocerasus), Gisela 5 (Prunus cerasus x Prunus avium) and MaxMa (Prunus mahaleb x Prunus avium)]. The results showed that increasing concentrations of NaCl and boron reduced shoots growth and length. PCR analysis of cherry root stocks demonstrated bands of all primers and band sizes to be 80-1000 bp. Polimorphism was observed in base sequence of genes that play a role in peroxidase synthesis of cherry rootstocks cultivated in different salt concentrations, and it came up with a rate of similarity in the 0.88-0.97 range. Also, peroxidase enzyme synthesis showed differences in plants cultured in the MS medium with high concentrations of NaCl, and no groups could be determined among varieties.