Capparis spinosa var. deserti Zohary (Family: Capparaceae), is an edible medicinal plant which is considered as an excellent genetic source of flavonoids. It is a threatened species that is listed among the endangered and unutilized plant species. In an attempt to preserve C. spinosafrom genetic erosion, micropropagation was employed as a useful way to mass propagate this plant due to the high population diversity and problems in traditional propagation methods. Furthermore, molecular and biochemical evaluation was carried out in C. spinosacallus under the influence of different chemical treatments.The best appropriate medium for proliferation of C. spinosashoot tip explants was Murashige and Skoog (MS) medium supplemented with 2.0 mg/l 2iP. An efficient procedure for inducing high frequency direct shoot organogenesis from leaf explants in response to thidiazuron (TDZ) is reported. TDZ at 0.75 mg/l induced shoot organogenesis. The effect of different concentrations of two elicitors; salicylic acid (SA), methyl jasmonate(MeJA) andthe precursor phenylalanine(Phe)on quercetin and rutinbiosynthesis was examined.Metabolic results were confirmed by elevated transcript level of quercetin and rutin biosynthetic genes, 4-coumaroyl CoA ligase and flavonol-3-O-glucoside L-rhamnosyltransferase in C. spinosacallus.This study provides useful data regarding the vital role ofplant growth regulators in conservation and micropropagationof C.spinosavar. deserti. Moreover,these results suggest that quercetin and rutin content in C. spinosa can be enhanced to a significant extent by SA, MeJA, and Phe treatments and the gene expression patterns ofqurecetin and rutin biosynthesis-related genes are regulated by these elicitors.