Species identifcation is fundamentally important within the felds of biology,biogeography, ecology and conservation. Te genus Geranium L. (Geraniaceae)comprises about 430 species distributed throughout most parts of the world.According to the most recent treatments, subg. Geranium is the largest subgenus with over 370 species classifed in ten sections. Te subg. Geranium is represented in Iran by 13 species. Tese species are grouped 3 sections. In spite vast distribution of many Geranium species that grow in Iran, there are not any available report on their genetic diversity, mode of divergence and patterns of dispersal.Terefore, we performed molecular (ISSR markers) and morphological studiesof 102 accessions from 13 species of Geranium (subg. Geranium ) that were collected from diﬀerent... habitats in Iran. Te aims of present study are: 1) can ISSR markers identify Geranium species, 2) what is the genetic structure of these taxa in Iran, and 3) to investigate the species inter-relationship? Te present study revealed that combination of morphological and ISSR data can identify the species.