Linum nervosum is among species that can hybridize with L. usitatissimum and produce fertile offsprings. Genetic diversity analysis of this wild relative of flax is important from conservation and breeding points of view. In the present study, 55 randomly selected plants of six different populations of L. nervosum varieties, including var. nervosum and var. bungei, were studied for morphological and genetic variability as well as population structure. Analysis of variance (ANOVA) did not show significant morphological difference between populations. PCA as well as PCA biplot confirmed that some morphological traits have taxonomic value. UPGMA clustering separated the populations of varieties in two distinct clusters, indicating degrees of morphological differentiation between them. Furthermore, UPGMA confirmed the variability in morphological characters within populations. Neighbor Joining tree and Neighbor-Net analysis of ISSR data revealed inter- and intrapopulation genetic variability. STRUCTURE plot revealed allelic difference of these varieties and some degree of intervarietal gene flow. K-means clustering showed the fragmentation of populations in support of AMOVA test, which revealed significant genetic difference among them. In general, obtained results confirmed the alternation of taxonomic level of L. bungei to the variety of L. nervosum.
