The environmental stress such as, salinity (soil or water) and drought are serious obstacles for medical plants and field crops in further areas of the world, especially arid and semiarid regions. In order to investigate salinity and drought stress on T. daenensis and T. kotschyanus germination indices, an experiment was carried out. To create salinity stress, sodium chloride (NaCl) at the levels of 0 (as control), -3, -6 and -9 bar, and for drought stress, polyetylenglycol 6000 (PEG 6000) in osmotic levels at 0 (as control), -3, -6 and -9 bar were used. Effect of drought and salt levels on investigated traits significant at 0.01. Result showed significance different between evaluated indices. Increasing of stress levels lead to reduction of germination and root and shoot length. Salt stress only in high levels reduced germination rate. Therefore, T. daenensis and T. kotschyanus have relative resistance to salinity in germination stage. Decrease in osmotic potential progressively inhibited seed germination of the two thyme species. In all salt treatments, maximum germination percentage in T. kotschyanus related to West Azerbaijan population and maximum germination rate related to Gazvin population. But in T. daenensis the highest values (both rate and percentage germination) were observed in Arak population. The germination rate of T. daenensis to the drought stress was more than the T. kotschyanus germination rate like the germination percentage. Comparing the two stresses, it appears that drought has more effect than salt in germination indices.