An efficient protocol for micropropagation was developed to conserve two rare Egyptian Capparis species; Capparis orientalis Duh. and Capparis leucophylla DC., using stem node sections and shoot tips. In vitro propagation of these two species has not been previously reported. Concerning C. orientalis; Murashige and Skoog (MS) medium containing 3 mg/L benzyl adenine (BA) with or without 0.2 mg/L 2-naphthalene acetic acid (NAA) were the most suitable media for the establishment of both stem node sections and shoot tips, and MS medium containing 3 mg/L BA was optimum for the multiplication of explants. Δ²- isopentenyladenine (2iP) gave promising results in enhancing elongation of axillary shoots of C. orientalis, when added to MS medium at a concentration of 1 mg/L in addition to 3 mg/L BA. The highest rooting percentage of C. orientalis (60%) was obtained on MS medium supplemented with 1 mg/L of both indole-3-butyric acid (IBA) and NAA after 60 days of incubation. With respect to C. leucophylla; MS medium containing 1 or 3 mg/L BA and that containing 2.5 mg/L of both BA and 2iP were the best for the establishment of stem node sections and shoot tips. MS medium containing 1 or 3 mg/L BA were the most promising media for the proliferation of explants. Gibberellic acid (GA3) at a concentration of 3 mg/L gave the best results in enhancing elongation of axillary shoots of C. leucophylla explants. The highest rooting percentage reached only 20% and was obtained on MS medium containing 2 mg/L IBA + 0.5 mg/L NAA after 60 days of incubation. An average of 92–98% of the acclimatized transplants of both C. orientalis and C. leucophylla survived after transferring into peatmoss:sand mixture (1:1 v/v) in the greenhouse conditions.