Geranium subg. Robertium (Geraniaceae) comprises eight sections, of which sect. Batrachioidea contains four species centred in Eurasia, Mediterranean region and the Himalaya Mountains. Three species of Geranium pusillum , G. molle and G. pyrenaicum occur in Iran show some degree of morphological overlaps that make the species delimitation difficult. Moreover, hybrids are known to be formed between these species elsewhere. Till present time, there has been no detailed information available on molecular phylogeny and genetic structure of these species in the country. Therefore, the present study was conducted with the aim to investigate species delimitation by both morphological and molecular data and to reveal genetic diversity and population structure in these three Geranium species. For this study, 216 randomly collected plants from 30 geographical populations in three Geranium species were used. We encountered extensive within species genetic and morphological diversity. ISSR molecular markers could not delimit the studied species. STRUCTURE analysis revealed the occurrence gene flow between these species. The Mantel test showed no correlation between genetic distance and geographical distance of the populations studied. Statistical analysis showed no significant difference between ITS and rbc L sequences and phylogenetic tree was constructed based on combined data set which separated outgroups from the studied species. Genetic affinity of the studied species has been discussed.