The leaf explants of Stevia rebaudiana were exposed to a range of EMS (chemical mutagen) and gamma radiation (physical mutagen) doses. Among all the treatments, doses of 0.4 % v/v EMS and 0.95 KR gamma radiation were found to be most effective treatment for selection of variants via direct shoot bud induction. The field-established plants designated as EMS (E), gamma (G), and control (C) plants were subjected to photosynthetic parameter studies where E and G plants showed lower chlorophyll content, transpiration rate, CO2 exchange rate, and stomatal conductance. The implanted field soil at the time of harvesting of plants showed reduction in organic carbon (OC), electrical conductivity (EC), phosphorus (P)/potassium (K), and total Kjeldahl nitrogen (TKN). The ISSR profiling of E, G, and C scored total of 107 bands out of which 63 % were polymorphic bands, and plant E was found to be more distant from the C plant phylogenetically. On phytochemical analysis, the G plant registered twofold enhanced rebaudioside A with lower stevioside (3.2 ± 0.22 % dry wt.) content, whereas E plant showed more than 1.5- and 2.0-fold increase in stevioside and rebaudioside A as compared to control plants. Both the E (3.1 ± 0.15 % dry wt.) and G (2.3 ± 0.21 % dry wt.) plants registered lower steviol. The enhanced steviol glycoside profile was supported by the RT-PCR analysis of UGT74G1 and UGT76G1 that corresponds to stevioside and rebaudioside A biosynthesis, respectively. While the E plant showed 5–6-fold increase in the UGT74G1 (RQ = 5.51 ± 0.5) and UGT76G1 (RQ = 6.61 ± 0.5) gene expression, the G plant showed 5-fold increase in UGT76G1 (RQ = 5.29 ± 0.2) gene expression.