Persian Zira (Bunium persicum) is one of the most important medicinal plants. RAPD technology was used to study the genetic relationships amongst 20 wild Persian Zira populations. We examined 15 populations from Iran, 2 populations from India, 2 populations from Afghanistan, and 1 population from Europe. This is the first investigational report on DNA extraction and molecular variation of Persian Zira. DNA was extracted using new modified CTAB protocol. In RAPD experiments, 26 primers were used and all of them produced polymorphism. A total of 146 reproducible amplified bands were scored and 96% (141 bands) percentages of polymorphic bands (PPB) was found. Data were analyzed with NTSYS and POPGENE programs. The MXCOMP module was then used to compute the cophenetic correlation. The matrix of generated similarities was analyzed by the UPGMA, using the SAHN clustering module and the dandrogram was drawn. Cluster analysis of similarity data, grouping of the landraces were studied according to their geographic origin. The genetic similarity ranged from 0.37 to 0.95. As anticipated, European population was separated from the rest of populations. And two distinct subgroups were formed at 0.50 similarity for these 19 populations (Non-European populations). One subgroup consisted of Iranian populations, and the second, non-Iranian populations, which contained two populations from Afghanistan and two populations from India. At a higher level of similarity (0.70), Iranian group was divided in two clusters and the populations of the each province were classified in the same group. Furthermore, grouping by morphological characteristics was compared with the results from RAPD analysis, and a significant correlation was produced. Finally, the investigation of the genetic variation of this plant with RAPD indicated that this marker is suitable tool for assessing polymorphic loci and estimating the genetic distance

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