Fraser photinia (Photinia×fraseri Dress.) with its impressive leaf colour is an evergreen woody ornamental plant that has commercial importance. Due to the rooting problems faced in the traditional vegetative propagation of the species, biotechnological methods such as plant tissue culture is used as a complementary strategy to propagation. Moreover, medium and long-term (cryopreservation) preservation of the species also gained importance recently as photinia has economic importance. However, occurence of risk of possible genetic variation between the donor plant and cryopreserved individuals after cryopreservation, reveals the necessity of assessment of genetic stability of the long-term preserved species. Therefore, genetic stability of the plantlets proliferated from cryopreserved fraser photinia shoot tips was assessed by two retrotransposon-based molecular markers (IRAP and REMAP) in addition to the optimization of cold hardening stage of the cryopreservation. 52.1% of mean polymorphism (mean PIC value is 0.307) was found between donor plant and clones by IRAP analysis while 47.2% of mean polymorphism (mean PIC value is 0.353) was detected via REMAP. According to the results of observed with these two marker systems, applied cryopreservation protocol caused an reasonable polymorphism (PIC value).