Cistus creticus L. (rockrose), a species of ecological and medicinal significance, constitutes a valuable component of the Mediterranean ecosystem. The present study investigated the effect of the inorganic salt concentration of Murashige and Skoog medium (MS), woody plant medium (WPM), and Driver and Kuniyaki Walnut medium (DKW) at several strengths (1/8×, 1/4×, 1/2×, 1×, and 2×) on the in vitro growth and organogenesis of rockrose. Significant interactions were observed throughout the experiments between pairs of plant origins, medium types, and strengths, and we also examined the extent to which they affected the studied traits was examined. The types of nutrient medium affected all studied traits except shoot and root percentages. The maximum growth percentage (143.49%) was gained using full-strength WPM. The best performance in shoot percentage was obtained using MS (100%) at several strengths along with 1× WPM (100%). The topmost rooting percentage values (98.61%) were obtained using 1× WPM and 1/2× DKW. The highest number of shoots and roots were observed using full-strength MS (9.39) and half-strength WPM (6.49), respectively. The maximum values for shoot and root length were achieved using 1/2× MS (0.78 cm) and 1/8× WPM (1.55 cm), respectively. The origin of the plant material did not influence any studied trait. Moreover, the genetic relations among the populations used in the in vitro culture were assessed using simple sequence repeats (SSR) markers. Twenty-eight alleles were identified across all five STR loci. The different and effective alleles per locus were 5.60 and 4.72, respectively. The average observed and expected heterozygosity was estimated at 0.52 and 0.72, respectively. Shannon’s information index and the inbreeding coefficient (F) were assessed at 1.48 and 0.30, respectively, revealing a narrow genetic base and high genetic similarity among origins, suggesting that they belong to the same population.