Investigating genetic diversity in plant species provides a platform for further insight in plant breeding and conservation. Therefore, in the present study genetic diversity of 13 geographically isolated genotypes of Zhumeria majdea, as a seriously endangered medicine plant growing exclusively in Hormozgan province (South of Iran) was studied. To do so, the leaf samples of Z. majdea were collected from the main growing habitats of this spices including Haji Abad, Geno and Bastak regions. The collected leaf samples were subjected to DNA extraction followed by PCR assay, using Inter-Simple Sequence Repeats (Issr) markers. Twelve markers produced totally 121 polymorphic bands and revealed a clear-cut among and within Z. majdea genotypes. The analysis of molecular variance (AMOVA) showed 86% and 14% variations within and among populations, respectively. Cluster analysis divided genotypes into four main groups. The first and second principle coordinates allocated 28. 81% and 15. 71% of the variations, respectively. In addition to the innate differences of the individuals, the high intra population variation of Z. majdea, can also be explained by differences in the presence or absence of endophytes and differences in the type and genetic pattern of their endophytes.