Background and Purpose: Common ash (Fraxinus excelsior L.) is a species with a widespread distribution in Europe. It mostly grows on mesophyll sites, mainly in karst valleys and by forest creeks, and in Herzegovina at northern expositions and higher altitudes with somewhat better types of soil. Materials and Methods: We studied 10 natural populations. We collected dormant buds with branches from 24 trees, randomly selected, but equally distributed in the population. We used six pairs of highly polymorphous microsatellite loci for identification and verification of genetic differentiation (FEMSATL 04, 10, 11, 12, 16 and 19). We additionally analyzed integration between genetic and ecological data for the area where material was selected, and also defined genetically homogenous areas of common ash. Results and Conclusions: The research of intra-population genetic structure pointed at the presence of a high level of polymorphism. Confirmation for such high polymorphism is in populations with approximately 10.2 alleles per locus (N) of the observed heterozygosis (Ho), while in the expected heterozygosis the values were considerably higher. Analysis of the inbreeding coefficient showed the value of 0.312, which demonstrates the presence of inbreeding in investigated populations. In this study we obtained a very low value of differentiation between populations, with the FST value as low as 0.023; this value measures the proportion of the total genetic diversity due to differences among populations. By correlation of the obtained microsatellite data and basic ecological parameters, climate for instance, common ash was grouped into two groups. The remaining five studied populations could not be grouped to either of these two, or a separate one, and they represent autonomous genetic units.