Rosa damascena Mill. is commercially the most important rose species used to produce essential oils. The plants of this species, cultivated in the district of Western Macedonia (Greece) for rose oil production, originated from indigenous genotypes but also nurseries abroad, mainly from Bulgaria. The present study investigated the genetic relationship between nine genotypes of R. damascena from Greece, one genotype from Turkey, three genotypes from Bulgaria and three genotypes from France using the molecular markers ISSR and SCoT. Also, the rooting ability of shoot cuttings from these nine genotypes was investigated by applying 2 g/L of the rooting regulator K-IBA. In addition, petals were chemically analyzed using GC-MS and LC-MS to identify the compounds that are the main components of the rose oil. The nine rose genotypes of R. damascena, cultivated in Greece, one from Turkey and one of the three genotypes from Bulgaria were clustered in one clade in the dendrogram. The other two genotypes from Bulgaria were clustered in a separate clade that demonstrated the existence of genetic diversity among the three Bulgarian genotypes, while the French genotypes were clustered in a third clade. The shoot cuttings rooted relatively easily (55–70%) with the application of K-IBA, without any significant differences among the nine genotypes. Large variation was observed among the nine genotypes in the main volatile compounds of the flower petal extracts, which are related to rose oil components. For these compounds, the concentrations in μg/g of the fresh petal weight were 2-phenylethylalcohol (1148.35–2777.19), nerol (27.45–64.93), citronellol (88.45–206.59), geraniol (69.12–170.99) and nonadecane (209.27–533.15). Of the non-volatile compounds, gallic acid was the most abundant phenolic acid in the petal extracts of the nine genotypes (0.28–0.82 μg/g), while for the flavonoids, quercetin and kaempferol variations of 0.35–1.17 μg/g and 0.26–2.13 μg/g were recorded, respectively.