Bunium persicum (Boiss) is a valuable medicinal plant native to Iran which grows wild in various parts of Iran. In the present study, genetic diversity was investigated within and among some populations of B. persicum collected from the main growing areas of this plant in Iran using RAPD markers. Fifteen RAPD primers produced a total of two hundred and twenty-nine bands, with two hundred and sixteen (94%) polymorphic bands between single plants of six investigated populations. Popgene softwarewas used to describe population structure thought calculation of Shannon's information index and Nei's gene diversity analysis. Genetic diversity within a population from Ghazvin Province was more than other populations and, within it, the population of Saghafy was less than others. Calculation of the ratio of the effective number of alleles to observed number of alleles within each population showed that the populations had equal distributions in agreement with the Hardy-Wienberg equilibrium. Also, a high Fst index derived by this study showed that the populations investigated were completely different from each other and had independent evolution. In UPGMA derived dendrogram based on the Jaccard similarity matrix, in most cases different individuals belonging to the same population were represented in different groups, showing a high level of genetic variation within all populations. The available genetic diversity of B. persicum must be considered in domestication, breeding and conservation programs.