L. amplexicaule L. grows in different regions of Iran and forms several populations that can be invasive in some area. Morphological and genetic variation of L. amplexicaule in Iran was studied to evaluate the differentiation among three presumed varieties within this species. Morphometric study was accompanied by the analysis of ISSR and chloroplast genome (psbA-trnH). Results of the molecular methods show that L. amplexicaule var. bornmuelleri Mennema. does not form any genetically distinct group. Genetic study of 103 plant specimens of 13 different populations using ISSR molecular marker revealed a high degree of within-population (67%) and among (33%) populations genetic diversity. AMOVA and Gst analyses produced a significant difference. Nm estimation revealed certain degree of gene flow/shared alleles between these populations, indicating that L. amplexicaule is predominantly an out-crossing species in Iran. Mantel test produced significant correlation between genetic distance and geographical distance of the studied populations (r = 0.097, P = 0.04). STRUCTURE plot identified two main gene pools for this species in Iran.