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Assessing genetic diversity of narrow endemic plants is essential for their conservation. Gymnospermium scipetarum subsp. eddae (Berberidaceae) is an Italian endemic limited to a narrow forest area in the southern Apennines. Here we used random amplified polymorphic DNA (RAPD) markers to investigate population genetic differentiation and diversity in relation to distribution and microhabitat conditions. In all five extant populations and 134 individuals analysed we found a relatively low level of population genetic diversity (average Shannon-Weaver diversity index = 0.280; mean percentage of polymorphic bands = 57.45%; mean Nei's gene diversity He = 0.187). Percentage of polymorphic bands (PPB) at species level was higher than at the population level (83.33%), while total species diversity (He = 0.210) was comparable to that found in the two southernmost subpopulations. AMOVA revealed a weak differentiation among populations, which shared three genetic pools in their genetic structure. The estimated gene flow among populations was relatively high (mean Nm = 5.320), while the Mantel test revealed no significant correlation between geographical and genetic distances at the population level. We argue that information on genetic diversity of G. eddae have important implications for conservation programmes, particularly for the establishment of ex-situ collections and restocking conservation actions. [ABSTRACT FROM AUTHOR]