Rodent tuber is an Indonesian anticancer herbal plant whose genetic variation is low. Genetic variation is crucial to be increased to increase the content of anticancer bioactive compounds. In vitro calli of rodent tuber had been mutated by gamma irradiation. Mutant plants had their genome modified and therefore also affected protein expression. The purpose of this research is to identify protein expression differences between mutant and control rodent tuber plants by 1D and 2D PAGE. 1D PAGE had shown differences in the number of protein bands between control and mutant. M6/2 did not show any expression of 6,9 kD protein. 2D PAGE had identified 24 proteins which were expressed by control and M6/2 plants. Among them, 13 spots were up-regulated and 9 spots were down-regulated in M6/2 plants. In conclusion, 1D and 2D PAGE analyses had successfully proven the changes in protein expression between control and mutant rodent tuber plants.