Abstract: In this study, molecular and morphological variation of 22 population of Plantago ovata assessed using RAPD, ISJ and agro-botanical markers. Field experiment was conducted in completely randomized block design whit four replicates. Principal component analysis and clustering based on distance between means of 8 morphological traits were used to detect relationship between accessions. Thirty five RAPD primers produced 142 polymorphic bonds, average 4.05 for each primer. Clustering analysis technique based on RAPD using Unweighted Pair Group Method shown that a closely association exist among morphological and RAPD dendrograms while didn`t exist any accordance between ISJ-GS with RAPD and morphological variation. In RAPD–based clustering, all population that was belonged to near area formed closely groups. The ISJ system marker produced 95 DNA fragment with 2.55 polymorphic bands for each semi-random primers. The dendrogram based on ISJ marker did not have accordance with geographical, morphological and RAPD variation. The result of this research verified possibility of use of RAPD and ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in Plantago ovata.