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This study evaluated the genetic structure, on a small spatial scale, of Campanula pollinensis along a heterogeneous altitudinal gradient on the Apennines of southern Italy. This endemic species inhabits territories in the Pollino National Park and is classified as a taxon of ‘Least Concern’. Along the elevation transect of Mt Cozzo del Pellegrino, the genetic profile of three subpopulations was examined using nuclear (ISSR) and chloroplast (SSR) markers. The subpopulation of the more elevated site showed maximuzm ISSR and minimum cpSSR diversity, while the opposite was found in the other two subpopulations. Differentiation values between subpopulations were indicative of restricted gene flow. The pollen flow/seed flow ratio suggested that pollen movements are less efficient than seed movements. At the same time, the haplotype pattern found along the altitudinal gradient could be the consequence of historical events, like the Quaternary glaciations. This study demonstrates that the use of two different markers can reveal some form of diversity even in small and apparently marginal patches of individuals. Consequently, a correct management of C. pollinensis ought not to neglect these small subpopulations, which are worthy of attention since they contain a relevant proportion of the total gene pool at this local scale. [ABSTRACT FROM AUTHOR]