Cedrus brevifolia (Cyprus cedar) is a narrow endemic species of the Cyprus flora. The range of the species has nowadays been limited to only one population, which is non-uniform and has been restricted to five neighbouring stands (patches) in the region of the Pafos forest. Although C. brevifolia is an endemic species with a narrow distributional range, it exhibits high genetic diversity. Based on this result, the species does not appear to be characterised by founder effect. The high genetic diversity also suggests that no bottleneck occurred during the different glaciations or climatic periods, as well as that the effective population size never dropped below a certain critical threshold. Thus, no evidence of negative effect due to genetic drift was found. The present results are a new example in which endemism can be associated with high genetic diversity. The C. brevifolia population, despite its narrow distribution, recorded low but significant genetic differentiation among the fragmented patches, as well as different patterns of population structure. These results imply that the identified separate patches could be regarded as subpopulations, which most likely resulted from the fragmentation of a previously common population. The large- and fine-scale patterns of spatial genetic structure in this narrow population are also unanticipated. At large-scale, correlation between geographical and genetic distances among subpopulations was observed; at fine-scale, different patterns of spatial genetic structure were detected, as the effect of the different patterns of gene dispersal at short distances.