<p>The Damask rose (<i>Rosa damascena</i> Mill.) is a woody perennial flowering plant recognized for its various commercial and medicinal benefits. A key goal of any plant tissue culture program is to achieve genetically stable plantlets. In this study, we employed two techniques-inter-simple sequence repeat (ISSR) and start codon targeted polymorphism (SCoT) markers-to assess the genetic stability of micropropagated plantlets of the Rosa (cv. Garaban). Our results indicated that the SCoT markers amplified 81 fragments, of which 21 were polymorphic, while the ISSR markers amplified 58 fragments with 14 polymorphic ones. A comparison of the mean values for informativeness parameters showed that the SCoT technique was more effective than ISSR in detecting genetic stability. Regarding the culture medium, the regenerated plantlets grown in media with the same concentrations of GA3, BA, and NAA exhibited the lowest values for genetic variation parameters. Therefore, this combination of plant growth regulators is recommended for commercial purposes. The results of RT-PCR analysis revealed that the expression patterns of two important flowering-related genes, <i>AP1</i> and <i>LFY</i>, were influenced by different concentrations of growth regulators. Specifically, the highest number of transcripts for these genes was observed in plantlets regenerated under the influence of NAA and BAP at 5&#xa0;mg&#xa0;L⁻¹. In conclusion, our findings provide valuable insights for the propagation of <i>Rosa</i> plantlets with minimal somaclonal variability. Additionally, the upregulation of <i>AP1</i> and <i>LFY</i> genes may help reduce flowering time in in vitro culture conditions.</p>