Because of increasing saline lands and decline the desirable agricultural lands for cultivation, the identification of salt-resistant medicinal plants is in high priority. For this purpose, an experiment was conducted to identify sustainable ecotypes of fennel at three levels of salinity stress in the greenhouse of the Faculty of Agriculture, University of Birjand, Iran, during the years 2014-15. The experiment was performed as factorial based on a randomized complete block design with two factors. A) 10 ecotypes as: Sardasht, Saghez, Kerman, Tabriz, Sabzevar, Rum, Khousf, Bojnord, Mashhad and Shabesta and B) three salinity levels: 3, 6 and 9 ds/m of Nacl with three replications. The results showed that, the salinity levels of 3, 6, 9 ds/m explained 72. 0, 69. 1 and 65. 2% of the total variation using GT (Genotype × Trait) Biplot, respectively. Similarly, for total of salinity stress GT-Biplot explained 65. 2% of total variation. Using polygonal diagram of genotype × trait, in stress 3 ds/m, the highest variation explained by ascorbate peroxidase, chlorophyll a and total chlorophyll, in stress 6 ds/m explained by superoxide dismutase, in stress 9 ds/m explained by chlorophyll a, chlorophyll b, total chlorophyll and superoxide dismutase and in the total salinity stress levels explained by chlorophyll a, chlorophyll b, total chlorophyll and superoxide dismutase, respectively. For all of stress levels, Tabriz ecotype for catalase, proline and malondialdehyde content, Mashhad ecotype for chlorophyll a, chlorophyll b, total chlorophyll and ascorbate peroxidase and Rum ecotype for superoxide dismutase were superior to other ecotypes, respectively. Based on all traits and in all environments, Mashhad ecotype was better and more stable than other ecotypes.