In vitro propagation of C. morifolium cv. ‘ Homa’ and cv. ‘ Delkash’ and wild C. coccineum via direct and indirect organogenesis and somatic embryogenesis were investigated. BAP at 0, 1, 2 and 3 mg l-1 or NAA at 0, 0.05, 0.1 and 0.2 mg l-1 concentrations were used to induce direct and indirect organogenesis of shoot tip explants. To study the callus induction and somatic embryogenesis, the young leaf explants were cultured on MS medium containing BAP (0, 1, 2 or 3 mg l-1) and 2,4-D (0, 1, 2 or 3 mg l-1). Direct shoot regeneration was achieved from shoot tip explants of ‘Homa’ and ‘Delkash’ as well as C. coccineum. The highest number of shoots through direct regeneration (13.78 and 8.89 shoots per explant for C. coccineum and C. morifoilum ‘Homa’, respectively) were observed in the treatment with 2 mg l-1 BAP and 0.05 mg l-1 NAA. In both species, the highest frequency of callus formation and embryogenesis were obtained on medium containing 2.0 mg l-1 2,4-D and 2 mg l-1 BAP. Genetic fidelity of 10 acclimatized plants derived from direct regeneration of each species was confirmed using six inter-retrotransposon amplified polymorphism (IRAP), inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) primers. A total of 56, 56 and 39 fragments were amplified for IRAP, ISSR, and SCoT, respectively. In general, our results showed that finding a better response of explants to embryogenesis or organogenesis in a specific cultivar and with special PGRs combinations and concentrations play an important role in the in vitro propagation efficiency of chrysanthemum species.