Lily flower with a high economical potential, is one of the most important flowers between horticultural and ornamental crops in worldwide and occupies the fourth place among flowers. In order to investigate the effects of different concentration of Chitosan (0 (control), 50, 100 and 150 and 200 mg/L) on regeneration and secondary metabolites production of two species of lily (L. ledebourii, L. dandie) in MS medium, an experiment was conducted based on a completely randomized design with 10 replications. The results of analysis of variance showed that chitosan significantly (P≤0.01) affected most of the morphological traits such as fresh weight, plant height, root numbers, bulblet numbers, percentage of regeneration, chlorophyll b, a and total and secondary phenol metabolites. The effects of chitosan on flavonoid was significant at 5% level. The mean comparison also revealed that the highest number and weight of bulblet in lilium ledebourii species was observed on MS medium containing 200 mg/l chitosan. However, the highest amount of plant height, root number, percentage of regeneration, chlorophyll a and b, total phenol and total flavonoid also was obtained in Lilium dandie species treated by 200 mg/l of chitosan. In conclusion, our findings highlight that the chitosan can positively affected regeneration of some lilium species.