Genetic diversity was determined and compared by using 86 random amplified polymorphic DNA loci in 450 families originated from 18 Pinus brutia Ten. (Turkish red pine) seed sources. These seed sources were sampled at three different categories and included six seed stands from six different breeding zones and six seed orchards, and six plantations which were originated from the respective seed stands. Genetic diversity parameters among the plantations, seed orchards and seed stands were compared. There was no significant difference in genetic diversity parameters of seed sources, but the percentages of polymorphic loci were slightly higher in seed orchards than their natural counterparts. These results suggest that through phenotypic selection practiced genetic diversity residing in natural stands seems to be successfully captured in seed orchards. Mean F-ST values (F-ST = 0.10-0.11) did not vary among three different categories of seed sources. Seed orchards (F-IS = 0.03) and plantations (F-IS = 0.07) showed reduced locality inbreeding coefficients compared with seed stands (F-IS = 0.13). The dendrogram of seed stands based on genetic distances did not produce any clusters of populations that could be attributed to their geographic proximity. A representative portion of genetic diversity existing in natural populations of Turkish red pine appears to be captured in established seed orchards and plantations with seeds from seed stands. (c) 2006 Elsevier B.V. All rights reserved.