Origanum is one of the most important medicinal plants used worldwide due to the economic importance, quantity and quality of essential oil and antioxidant properties. Drought is one of the major abiotic stresses that cause deleterious damage to plants. As a bio-elicitor, chitosan prevents severe damage to plants under stress conditions by triggering plant defense mechanisms. To investigate the effects of chitosan application and water deficit stress on growth, yield and secondary metabolites of origanum, a greenhouse study was performed in a factorial experiment based on randomized complete block design (RCBD) with three replications. The studied factors consisted of foliar application of chitosan at three levels (0, 250 and 500mg/L), under well-watered and water deficit stress conditions in two origanum species (Origanum majorana and Origanum vulgare). The application of water deficit stress and foliar treatment with chitosan (three steps) was performed three weeks before flowering. Results showed that the water deficit stress reduced the plant dry weight, while increased total phenol and essential oil contents. However, foliar application of chitosan at 500mg/L under water deficit stress conditions increased dry weight of shoots, and phenol content. Application of chitosan at 250mg/L increased the content of essential oil compared to the control. Results also showed that application of chitosan as a bio-elicitor can reduce the adverse effects of water deficit stress on marjoram plant. The analysis of GC/MS apparatus revealed that 33 compounds were identified in essential oil, in which γ-terpinene, cis-sabinene hydrate and terpinolene were the dominant in the oil of both origanum species.