Species range expansions and (re)colonization of landscapes variously dominated by humans occur on a global scale. Understanding such range enlargements and subsequent changes in the composition of ecological communities is important for conservation management, and the golden jackal (Canis aureus) can be considered a model species for regional and continental range expansion. Although this mesopredator has been known from the Adriatic Coast of southeastern Europe for over 500 years, the species is a recent arrival further north, including in Slovenia where jackals were first confirmed in the 1950s. Research from eastern Italy found jackals with ancestry from the Dalmatian region on the Adriatic Coast and the Pannonian region further east. We predicted similar ancestry for Slovenian jackals, and examined samples from Croatia, including Dalmatia and interior regions, Serbia, Hungary, and Slovenia with 25 microsatellite markers to determine population genetic structure. We detected two distinct genetic clusters, representing the Dalmatian and Balkan-Pannonian (Pannonian) jackal populations (F-ST = 0.157, 95% CI: 0.112-0.209). Contrary to expectations, only few individuals in Slovenia exhibited signs of Dalmatian ancestry, and none appeared to be direct immigrants. Some results suggested a third cluster centered in northern Hungary. These divergent profiles might indicate immigration from outside the study area, and samples from regions further east are required for additional resolution. Based on our results, we hypothesize that Dalmatia has not been a substantial source for recent range expansion of the species, which has likely occurred from the east. Further investigation can help resolve the ancestry and current distribution of the Dalmatian and Pannonian populations, and the ecological relationships resulting from progressively overlapping distributions of canid species. Finally, genomic research could illuminate whether genetic variants from eastern areas might have facilitated jackal expansion into regions characterized by a colder climate, the presence of snow, and extensive forest cover; habitats seemingly avoided by the jackals occupying the Adriatic Coast and surrounding areas in southeastern Europe.