Water stress is one of the most important environmental abiotic stress that reduced crop yield especially in arid and semi arid regions of the world. In order to identifying drought tolerance, 39 cultivars of spring, facultative and winter type wheat varieties were planted as subplots within the irrigation plots (main plots) in a randomized complete block design with three replications in a research filed of Faculty of Agriculture, University of Mohaghegh Ardabili, Iran. In 2/3 continuous irrigation stress level, based on stress susceptibility, geometric mean productivity and harmonic indices, 'Sepahan' , 'Karaj 3' , 'Bahar' and 'Yavaroos' were known as the best varieties; and in 1/3 continuous irrigation stress level, based on the mentioned indices, 'Hirmand' , 'Bahar' , 'Yavaroos' and 'Marvdasht' were the best one. According to biplot resulted from principle coordinate analysis, in 2/3 continuous irrigation 'Moghan 1' , 'Golestan' , 'Kavir' , 'Maroon' , 'Karkheh' , 'Chanaab' , '10' , '6' , 'Bahar' and 'Sepahan'; and in 1/3 continuous irrigation 'Golestan' , '10' , 'Niknejad' , 'Maroon' , 'Darab' , 'Falat' , ' Arta' , 'Marvdasht' , 'Bahar' and 'Hirmand' were identified as the most tolerant cultivars. According to multiple regression analysis in subject of agronomic traits, 43, 33 and 25 informative ISSR markers identified in control, 2/3 and 1/3 continuous irrigation conditions, respectively. Also among these markers, there were significant relationship between P 12 L 3 and P 21 L 3 markers with plant height and spike length; P 4 L 1 and P 22 L 1 markers with flag leaf length; P 19 L 4 markers and number of node; P 30 L 4 markers and awn length; P 10 L 1 and P 22 L 1 with peduncle to plant height ratio in all of stress and non-stress conditions.