Medicinal plants play important role in communities hygienic and health, both in terms of disease cure and preventing. Medicinal plants in Iran serve as valuable genetic resource. Among these plants, Fennel ( Foeniculum vulgare Mill.) belonged to Apiaceae family has received great deal of attention. The previous studies in Iran and worldwide have mentioned enormous properties for fennel. Various climate conditions in Iran, fennel has high genetic diversity. So, managing of genetic resource, knowledge of intra and interspecific diversity will help getting information about evolutionary processes and genetic erosion about this valuable species. The most principle goal to conduct this research is to evaluate genetic variation of fennel endemic accession using molecular marker of SRAP and also ltr" Keywords : Fennel, SRAP, GC/MS, Principle Coordinate Analysis, Trans anetole