Juniperus communis var. saxatilis is a short prostrate evergreen conifer that grows on dry hills in the mountain areas. In the Balkans, this taxon has a fragmented distribution. Both leaves and cones are rich in essential oils (EOs), which play an important role in plant interaction with the environment. Even though leaves and berries represent a significant source for humans and wildlife, there is no research on the genetic and EO variability in the region. In this paper, we analysed individuals from eighteen populations from the entire Balkan Peninsula. Three bioclimatic regions were identified, based on precipitation and temperatures. Amplified fragment length polymorphism (AFLP) data revealed high genetic variability, which is mostly located within the populations (91.7%). In total, 156 compounds representing 99.0% of total oil were detected and identified. Three chemotypes (ɑ-pinene, sabinene and δ-3-carene) were detected in all samples. While all chemotypes could be detected throughout the region, their distribution was correlated with environmental factors. The influence of environmental variables on EO composition and chemophenetics are discussed.