The increase interest and study of underutilized and neglected crops is actual for the last years. In the study, the restriction polymorphisms of GBSSI and SSSI gene in gamma-irradiated mutant lines of amaranth was performed. To evaluate polymorphisms of restriction sites endonucleases AciI, BsaJI, FatI EcoRI, BamHI, PstI, HpaII and PciI were used. GBSSI gene responsible to amylose synthesis was digested with HpaII and PciI restriction endonucleases. Two PciI restriction sites and three HpaII restriction sites were evaluated and any changes in restriction sites were recorded. Profile changes of the SSSI gene in mutant lines C 15/1 and C 236/1 were recorded after the restriction digest by BsaJI. Restriction cleavage polymorphism was recorded after the restriction digest of segment 5250-6854 bp with restriction endonuclease FatI, too.