Ziziphora tenuior L. and Ziziphora canescens Benth. are two of plants which using in folk medicine in the Kalamoon Mountains areas of Syria for cough, stomachache and dysentery. Samples of Ziziphora genotypes were collected from four different locations (Assal Al-Ward, Yabroud, Qarah and Maaraba), 20 RAPD and 12 ISSR primers were used to assess the genetic diversity of 10 genotypes. Amplified fragments were polymorphic with percentage 93.4% and 100% when RAPD and ISSR markers were used respectively. The first cluster depending on RAPD data formed by the grouping of all Ziziphora tenuior L. and the second cluster formed by grouping of all Ziziphora canescens Benth. genotypes. While the first cluster based on ISSR data formed by two genotypes Ziziphora tenuior L. (Maaraba), the second cluster formed by three genotypes Ziziphora tenuior L. and five genotypes Ziziphora canescens Benth. (Assal AlWard, Yabroud and Qarah). ISSR markers were recorded a high degree of biodiversity among Ziziphora tenuior L. genotype collected from Maaraba and other genotypes. Genetic stability of Ziziphora tenuior L. and Ziziphora canescens Benth. was confirmed among mother plant and shoots that underwent one to nine cycles of in vitro subculturing by RAPD markers that produced monomorphic bands, while ISSR bands were polymorphic especially in 7,8 and 9 subcultures. Also Genetic variations of Ziziphora canescens Benth. that resulted from salinity (1,2,3,4 and 5 g/L) and pH (7,8 and 9) media were detected, both of RAPD and ISSR bands were polymorphic compared with control except some RAPD primers produced monomorphic bands. Callus from Ziziphora tenuior L. that induction on different media (MS + 1.5 mg/L NAA + 0.5 mg/L Kin) or (MS + 2 mg/L IBA + 0.5 mg/L Kin) showed high variations compare with micropropagated plants from apical mirestem on media (MS + 1 mg/L Kin + 0.1 mg/L NAA).