Kochia scoparia (L.) Schrad are one of the wild species of with a good dispersion over lorestan province in west Iran. Due to the lack of information on the genetic diversity of Kochia scoparia (L.) Schrad, therefore, this study aimed to identify and genetic diversity efforts was made under the present study to 144 natural populations belonging to Lorestan province. RAPD and ISSR markers are useful in the research herbaceous. A total of twenty RAPD and ISSR primers produced of reproducible bands which 7713 produced which 6721 of them were polymorphic (87.13%), and 8376 produced bands that 7456 of them were polymorphic (89.01%) respectively. The total length of bands created between 285(P4) to 1710(OPC-09) bp fragment was variable. Matrix 1/0 bands RAPD and ISSR by MVSP ver 3.2 and NTSYSpc ver 2.02 clustering UPGMA of Jaccard coefficient and similar groupings were obvious in the PCoA analysis. The results showed the presence of Six separated genetic group among studied populations over Lorestan province. The highest genetic similarity coefficient (0.62) was observed between ASBs and NBs and lowest similarity was between NBS and DBS (0.14). This study genetically characterized the Kochia scoparia (L.) Schrad that might have a significant contribution to the genetic and ecological conservation of this important species, accordingly RAPD and ISSR markers were found to be useful for the assessment in genetic diversity studies of Kochia scoparia (L.) Schrad species.