Linum album L. is a medicinal species that show distyly. The present study was aimed to investigate morphological and genetic differences between long-styled and short- styled plant and if these differences vary with population’s genetic structure. For these reason, nine populations of L. album were collected from different regions of Iran. The obtained results showed that the long-styled and short- styled plants differed significantly in their morphological as well as genetic content (ISSR loci). Genetic analysis revealed that the genetic rearrangements in allelic forms and combination were associated with these plant forms differentiation. L. album genetic differentiation between the two morphs.