The maize line ChK-218 was created as a result of mutagenic treatment of the seeds of the line VIR-27 with streptomycin. Significant differences among these lines according to the size and number of heterochromatic regions in the various chromosome pairs have been demonstrated earlier. This paper provides comparative analysis of genomes of the VIR-27 and ChK-218 lines with SSR- and RAPD-PCR. The level of polymorphism extent reached 26,9 % in the case of SSR-alleles and 21,7 % in the case of RAPD-amplicons. The detected differences suggest that treatment of maize seeds with streptomycin makes considerable mutagenic effect which involves both structural chromosome changes and DNA sequence alterations.