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Genetic variations within the species of Agropyron desertorum and 2 varieties of A. cristatum subsp. pectinatum var. imbricatum and A. cristatum subsp. pectinatum var. pectinatum were studied using morphological traits and total protein profiles (with sodium dodecylsulphate polyacrylamide gel electrophoresis). An experiment was conducted in Research Institute of Forests and Rangelands (2012-2013) using a completely randomized block design with three replications. Means comparison of different agronomical traits among different wild populations of three taxa showed that A. desertorum had higher plant crown, plant height, panicle length, number of stems and plant dry matter weight; however, var. pectinatum had higher panicle length, grain yield and 1000-grain weight and got into the pollination and full flowering phases in a shorter period. The results of total protein profiles revealed that the genetic diversity of var. imbricatum samples was considerably higher than var. pectinatum and/or A. desertorum. Classification analysis of different populations of taxa using both markers showed that populations of var. pectinatum were closer to A. desertorum than var. imbricatum. The results demonstrated that the study of genetic diversity and the relationships among the crested wheatgrass species using agronomical traits and total protein profiles provides important information for the collection, genetic conservation and planning of future breeding programs.