Abstract Low-energy ion beam bombardment at energy levels in the range of 60–125 keV and ion fluences (dose) of 1 × 10 16–5 × 10 17 ions/cm 2 was chosen for mutation induction in Thai jasmine rice ( Oryza sativa L. cv. KDML 105) at Chiang Mai University. One of the rice mutants designated BKOS6 was characterized. The rice mutant was obtained from KDML 105 rice embryos bombarded with N + + N 2 + ions at an energy level of 60 keV and ion fluence of 2 × 10 16 ions/cm 2. Phenotypic variations of BKOS6 were short in stature, red/purple color in leaf sheath, collar, auricles, ligule, and dark brown stripes on leaf blade, dark brown seed coat and pericarp. The mutant's reproductive stage was found in off-season cultivation (March–July). HAT-RAPD (High Annealing Temperature-Random Amplified Polymorphic DNA) was applied for analysis of genomic variation in the mutant. Of 10 primers, two primers detected two additional DNA bands at 450 bp and 400 bp. DNA sequencing revealed that the 450 bp and the 400 bp fragments were 60% and 61% identity to amino acid sequence of flavanoid 3′hydroxylase and cytochrome P450 of O. sativa japonica, respectively.