Turkish red pine (Pinus brutia Ten.) is one of the important tree species in Turkey. The species has been heavily disturbed by anthropogenic factors and fire, making it important to understand the magnitude of the impact on genetic diversity of areas reserved for seed production. To explore the extent of genetic variation in Turkish red pine seed stands, a random amplified polymorphic DNA (RAPD) marker system was used in the study. The estimated genic diversity for seed stands was found to range from H=0.17 (P, %of polymorphic loci=%58.7) in Cameli-Goldag to 0.29 (P=%81.7) in Bayramic-Karakoy seed stand though the lowest polymorphism was observed in Findikpinari seed stand (P=55.8%). The total gene diversity was calculated as H-T=0.34, in Turkish red pine. About 65% of the total diversity was within seed stands. No distinct pattern of genetic diversity was found according to the geography, elevation or breeding zones. The highest genetic differentiation was found in the Western Mediterranean geographic region, however, within population genetic diversity was found to be similar among different geographic regions (H-S=0.22-0.24). G(ST) value calculated was high (0.35) indicating that genetic differentiation among the studied seed stands was substantial. Dendrogram constructed with genetic distance data did not yield a firm pattern with respect to geography, elevation and breeding zones. In fact, the most of the clusters in the dendrogram had very low bootstrap values, suggesting that the clusters could be refined if more populations and markers are included in the future studies. The implication of the results with respect to in situ conservation of genetic resources of the species was discussed.