Although the Balkan Peninsula belongs to the most mountainous regions of Europe, phylogeographic structure of its alpine flora remains insufficiently understood, especially for species distributed both in the western and eastern parts of the Peninsula. We analyzed Campanula orbelica, a Balkan endemic typical of high-mountain siliceous grasslands, based on the population genetic structure, climatic niche modeling at the species- and intraspecific level, and niche hindcasting back to the Last Glacial Maximum (LGM; 20 kya). Our data reveal a clear phylogeographic pattern with three geographically coherent genetic groups: (i) the most divergent and spatially restricted lineage of the Pirin mountains (east), (ii) neighboring Rila mountains and other eastern Balkan massifs (Rhodopes, Stara Planina, Vitoša), and (iii) the most geographically disjunct mountains of the Scardo-Pindhic range (Šar Planina and Korab) in the west. This pattern indicates multiple refugia and isolated evolutionary centers within the Balkan Peninsula mountains, with the eastern part of the range as likely ancestral area, and an early dispersion into the western region, which formed the main geographical disjunction. The genetic divergence was only partly correlated with geographical isolation, clear dispersal barriers, or climatic niche shifts, suggesting contrasting isolation/dispersal dynamics in various parts of the range. Climatic niche overlap was low among eastern vs. western groups, which correlates with the longest spatial distance and significant genetic divergence, while niche characteristic of the Pirin lineage was a subset of the adjacent Rila lineage niche. High genetic divergence of the Pirin populations was also not correlated with persistent gaps in potential distributions but hypothetically may have been triggered by diversified (limestone/silicate) bedrock conditions. Our results highlight the need for high-mountain phylogeographic surveys in the eastern part of the Balkan Peninsula, to assess the biogeographical relevance of isolation patterns and definition of evolutionarily important units in the high-mountain flora.