Abstract. Minaeifar AA, Sheidai M, Attar F. 2015. Genetic and morphological diversity in Cousinia cylindracea (Asteraceae) populations: Identification of gene pools. . Cousinia is one of the largest genera in the Asteraceae family. It contains 600 to 700 species distributed in Southwest and Central Asia. In Iran with 270 species it is the largest genus after Astragalus,. Cousinia probably is unique in the degree of diversification of all its parts and high numbers of species in restricted area. In this investigation 90 plant specimens of 10 geographical populations of Cousinia cylindracea Boiss. were studied from morphological and genetic (ISSR) points of view. Both intra and inter-population morphological and genetic variability was observed in the studied populations. ANOVA and CVA tests revealed significant morphological difference among these populations. Similarly, AMOVA tests revealed significant molecular difference among geographical populations. Mantel test produced significant positive correlation between genetic distance and geographical distance of the studied populations. Networking, STRUCTURE analysis and population assignment test revealed low degree of gene flow among these populations. The results identified two different gene pools of C. Cylindracea in Iran, supporting Rechinger suggestion that C. cylindracea might have two varieties in Iran.