Hops is an economically important species due to its diverse secondary metabolites and extensive use in the brewing and medicinal industries. Although hops is widely distributed in Kosovo, the chemical composition of its essential oils and genetic variability of wild populations remain understudied. Therefore, this study aimed to evaluate the chemical and genetic variability of Kosovo's wild hop population using essential oil constituents and microsatellite (simple sequence repeat - SSR) markers. Female hop inflorescences were collected from 21 wild populations in Kosovo. Essential oils were extracted from the dried plant material using a Clevenger apparatus. Chemical composition of the essential oils was analysed using GC-FID-MS. DNA was extracted from dried leaves, and 15 SSR markers were used for fragment analysis. The main constituents of the essential oil were myrcene, α-humulene, (E)-β-farnesene, α-selinene, β-selinene, and E-caryophyllene. Statistical analyses based on chemical composition of essential oils and SSR markers highlighted the low variability among populations and high variability within populations. These findings provide valuable insights for developing strategies for potential use and conservation of wild hop populations in Kosovo, laying the groundwork for future research and comparison with commercial cultivars to assess their breeding potential.