Linum austriacum L. (Linaceae) which is known as Asian flax is an herbaceous medicinal plant species that grow in Iran in different latitudes and forms some local populations particularly in the West and North-West of the country .Within-and between-genetic diversity in response to altitude changes was investigated in geographical populations of L. austriacum by using cytogenetic and ISSR molecular markers. These populations were diploid with 2n = 18 and differed significantly (P<0.05) in their mean chiasma frequency and chromosome pairing. Significant positive correlation r >0.90, P < 0.05) occurred between latitude and the mean number of quadrivalents. The highest level of genetic diversity parameters as Shanon Information Index and gene diversity occurred in Salavat-abad population. Moreover, the STRUCTURE analysis also identified this population as the most varied population This population had medium altitude distribution. Mantel test performed between genetic distance and geographical distance showed no significant correlation (R2 = 0.09, p = 0.39). Pearson coefficient of correlation determined between genetic diversity parameters and altitude, produced a significant negative correlation (r = -0.85, P<0.01) with the number of effective alleles. The present study revealed that Linum austriacum populations do have some cytogenetic and molecular variation in response to altitude.
