Abstract: Genotypes of the chrysanthemum cultivars Harman and Indianapolis were transformed using Agrobacterium tumefaciens strain LBA4404, which carries the binary plasmid pBIN19::Rd29A::ScTPS1TPS2::nos and pBIN19::35S::ScTPS1TPS2::nos, respectively. ISSR markers were used to discriminate two cultivars from each other, and independent transgenic plants generated in each cultivar. Firstly, the nptII gene and Tnos sequence in the transformed genotypes was confirmed by PCR. For genotyping, 10 ISSR profile markers produced 131 DNA bands. The percentage of polymorphism ranged from 20 to 82.4 %. Primer UBC 872 provided the highest percentage of polymorphic bands (PBP), polymorphic information content (PIC), marker index (MI) and resolving power (Rp). A positive correlation was found between the Rp value of each primer and the number of identified genotypes (r=0.822***). The UPGMA analysis generated two groups with a similarity coefficient of 0.67. The genotype grouping was confirmed by PCoA. The ISSR technique was efficient to discriminate transgenic cultivars from non-transgenic plants.