Stevia rebaudiana, is an economically important medicinal plant act as sweetener substitute for diabetic and obese people. Climate modification causes a considerable influence on the production of several secondary metabolites of plants.  In the present investigation, the effect of environmental factors on genetic divergence for three varieties of Stevia rebaudiana (Spanti; China and Eg1)  by using differential response for different climate modification (black net, white net and plastic cover in comparing to without cover treatment (control) was studied. Data indicated that the application of different modification treatments showed that the use of nets had significant effect on air and substrate temperature and light intensity as well as relative humidity. In the same context, vegetative growth traits and biochemical analyses for stevioside and rebaudioside content had significant effects according to climate modification treatments. Electrophoresis banding patterns of total protein and isozyme (peroxidase) were obtained to characterize genetic relationship for both different treatments and genotypes. Based on the resolved soluble protein profiles it could be detected 11 and 13 polymorphic unique bands for different treatments and genotypes, respectively. The percentage of polymorphism for all studied treatment and varieties was 100 %. 12 and 13 polymorphic bands were detected in Isozyme marker (peroxidase) analysis for different treatments and genotypes, respectively. However, black net treatment and Spanti variety has the highest polymorphism percentage 100% by using cluster analysis of banding pattern for examined treatments and genotypes based on similarity index and UPGMA resulted four distinct clusters.