In the present study, a genetic analysis of nuclear microsatellites was conducted in Abies cilicica populations growing in West Taurus, East Taurus, and Lebanon mountains to obtain evidence for significant genetic differentiation. Despite range fragmentation, all examined populations tended to maintain a relatively high level of genetic diversity (H E = 0.724) and showed moderate genetic differentiation (F ST = 0.134) that is frequently noted in Mediterranean tree species. However, significant inbreeding, bottleneck effect, and low effective population sizes were detected, that may negatively affect species genetic resources. Bayesian clustering revealed three distinct groups, "West Taurus", "East Taurus," and "Lebanon", which reflect geographic structure of the species natural range. Minor genetic admixture between Lebanese and East Taurus populations of A. cilicica was found, but no genetic admixture between Lebanese populations and West Taurus. We argue that significant genetic differentiation discovered among areas of species occurrence is probably due to the effect of long-lasting genetic isolation that started in that region along with the Pleistocene climatic alternation and was further enhanced with human-induced deforestations.