A micropropagation protocol was developed which may assist in the safeguarding and augmentation of dwindling natural populations of Clinopodium odorum (Griseb.) Harley, a critically and endangered medicinal plant. Factors affecting culture initiation bud sprouting and growth, rooting, and acclimatization were studied, using nodal segments of in vitro germinated seedling as primary explants on six media supplemented with different concentrations and combinations of 6-benzylaminopurine (BAP) (0.5–1.5 and 2-Naphthalene acetic acid (NAA) (0.5–1.5). Best results for culture initiation with sustainable multiplication rates (100%) were obtained on WP medium without any growth regulator. WP with the addition of 0.5:1 or 0.5:1.5) of BAP and NAA promoted a higher elongation; however, the optimum number of nodes were obtained in plantlets grown on 1/2 MS with the addition of 1:1.5 of BAP and NAA. Culture of sectioned individual nodes transferred to the media with different rates of BAP and NAA 1/2 MS-9 (1.5:1.5), SH-8 (1.5:1.0), and 1/2 B5-4 (1.0:0.5) media resulted in no proliferated shoots. The in vitro plants were successfully acclimatized garden soil and sand (2:1) in the greenhouse, with over 90% survival rate. The in vitro-grown plants could be transferred to ex vitro conditions and the efficacy in supporting ex vitro growth was assessed, with a view to develope longer-term strategies for the transfer and reintroduction into natural habitats.