The objectives of this study were to make morphological and molecular characterization of Turkish stevia accessions. The field data showed significant variations (P < 0.05) for all morphological parameters (plant height, number of main stems per plant, number of secondary stems, fresh and herb yields) exception with number of secondary stems. The primers of MtP5CS, AtNHX1, MtProDH, Mt-Actin MtSOS1and MtSOS2 genes were used as loci specific DNA markers. All markers were amplified in Stevia genome and provided a mean of 74.16% polymorphism rate. Flow cytometer analysis showed no statistically significant differences (P < 0.16) for 2C DNA content with a mean of 1.62 pg. The UPGMA analysis revealed that Samsun accession was distinctly separated from the others and had the lowest 2C DNA content (1.52 pg). This study first time showed that the stevia accessions grown in Turkey have limited genetic and no nuclear DNA content variations. The results also revealed that gene targeted functional markers associated with salt and drought tolerance have a great potential to be used as DNA markers to determine the genetic variation in plants