Two new varieties of Cryptocoryne willisii were developed through mutagenesis in this work, where shoot-tip explants of C. willisii were subjected to a range of 60Co gamma ray irradiations: (0, 100, 200, 300, 400, 500, 600, 700 and 800 Gray). The LD50 for the tissue culture plants of C. willisii was at 25 Gy, which was considered as an appropriate dosage to induced mutations in this plant. About two thousand shoot-tip explants were irradiated at 25 Gy and variants from the M1, M2, M3, and M4 generations were screened for morphological differences. The shoots were subcultured repeatedly until the 4th generation (M4) to ensure stability of mutants. Although initially many regenerants with different morphological traits were produced, only two mutants remained stable. The mutants obtained were dwarf plants (D1) and plants of taller stature with pigmented leaves (G1) in comparison to control cultures. This was verified from the significant F value from the ANOVA test, where P<0.05. The Inter-Retrotransposon Amplified Polymorphism (IRAP) markers were used to distinguish the D1 and G1 genomes from normal C. willisii genomes. The analysis revealed two specific bands 325 by and 420 by using Nikita primer for the D1 mutant and 240 by and 300 by using combination of 3'LTR primer and LTR 6149 primer for the G1 mutant.