Successful management and preservation of natural populations depend on accurate assessment of genetic diversity. Knowing the genetic diversity within a population is important for choosing the conservation strategies for the species. Geranium pusillum L. is an annual or biennial herb mainly native to Europe, northern Africa, and western Asia, and G. pyrenaicum Burm is a frost hardy perennial native to areas of France and Spain to the Caucasus. In general, taxonomic and biosystematic studies of Geranium are not known in Iran; moreover, in a few cases, inter-specific hybrids and intermediate forms are recognized. A detailed morphological, micro-morphological and molecular (ISSR) study of Geranium is done here with the following objectives: (1) to delimitate the species; (2) to carry out a population genetic study and produce information on genetic structure and genetic variability within each population in G. pyrenaicum and G. pusillum. The present study revealed that a combination of morphological and micro-morphological (seed and pollen) data can separate the species. In the present study, 84 randomly collected plants from 12 geographical populations of two Geranium species were considered. A consensus tree based on morphological and genetic data separated some of these populations from the others, suggesting the existence of ecotypes in the studied taxa.