Carum copticum is an medicinal plant growing in southwest and North West parts of Iran. Efficient and short protocol for indirect somatic embryogenesis of ajowan has been developed. All steps of in vitro regeneration from explant to hardening were described. Novel synthetic cytokinin 3-methoxy [-6-benzylamino-9-tetrahydropyran-2-yl] purine was successfully used for indirect shoot regeneration of ajowan. The genetic stability of regenerated plant was proved through flow cytometry.