Cordyline fruticosa is a medicinal plant that is also ornamental due to its variegated coloured leaves. Some traits benefit from mutation. Guanidine hydrochloride and sodium azide were the chemical mutagens used in this study. For each, concentrations of 30, 40, and 50 mM were used. The plantlets were exposed to these mutagens, and the explants were cultured in vitro using micropropagation. To estimate the effect of mutagens in comparison to non-mutant (control), different 8 morphological characters were measured. In the case of guanidine hydrochloride, all of the treatments are nearly identical to control, with no significant differences except for 30 mM, which is lower than the others. Cordyline fruticosa genetic variation resulted in a wide range of polymorphism percentages. In the case of sodium azide, it was 74.66 %, while in the case of guanidine hydrochloride, it was 37.77 %. All morphological parameters decreased in sodium azide comparing to control, with the exception of the number of branches, which increased more at 50 mM than at other concentrations and control. All morphological parameters increased in mutants rather than controls, unlike guanidine hydrochloride. For photosynthetic pigmentations, all pigments decreased with sodium azide treatments. As a result, chemical mutagens cause genetic instability and variation, which manifests itself in morphological and physiological characteristics.