This study explores the population structure, hybridization, and adaptation of Juniperus communis sensu lato in the context of its current habitat fragmentation, using inter-primer binding site markers and needle morphometry. Three native juniper taxa in Slovakia were analyzed: J. communis ssp. communis, J. communis ssp. nana, and their putative hybrid, J. communis nothovar. intermedia. The results reveal a moderate overall structure (Φ