The rebaudioside-A/stevioside (R/S) ratio influences the breeding and commercial values of stevia genotypes. Three stevia genotypes, “High Sugar,” “Levan,” and “ShouA3-2,” with respectively high, medium, and low steviol glycoside (SG) contents were investigated to answer the following questions: how do SG contents change when NaCl induces gene expression? Is SG-content positively correlated with NaCl tolerance? Does the genotype, with a high R/S ratio, exhibit higher expression of SG genes; compared to the genotype, with a low R/S ratio? Growth parameters, through our results, were decreased in “High Sugar” and “ShouA3-2” relative to “Levan” who showed better performance under the severe 200 mM NaCl treatment. Extendedly, “High Sugar” decreased the expression of SG-genes (cpps, ks, kh, and ugt74) under the low 50 NaCl treatments, while the “ShouA3-2” has upregulated all the genes (except ks) under the moderate (100 mM) NaCl treatments. Overall, the antioxidant sod1 gene was upregulated, similarly, the “Levan” has upregulated the cpps, while differentially expressed ks and kh across the NaCl treatments. In conclusion, high R/S ratio does not necessarily mean enhancement in responses to abiotic stresses in stevia. The R/S ratio in stevia does not solely rely on the expression of SG-pathway genes thus; other ancestral genetic elements may independently regulate them. Under salinity, the rooting characteristics improved when R/S ratio was low, while when moderate the shooting characteristics were superior. We recommend breeding for moderate R/S ratios to assure probable resilience to challenging climates (such as salinity) and potent higher agronomic traits.