Clonal variation in the production of female and male strobili was studied in seed orchards of Pinus brutia in southern, and those of R nigra and R sylvestris in northern Turkey. Large differences in female and male fertility among clones were found. The most abundant quartile of clones in R brutia, R nigra and R sylvestris seed orchards produced 44.1%, 40.5%, 33.9% and 37.8% of total female, and 76.1%, 62.6%, 36.7% and 34.1% in total male strobilus production, respectively. There were positive correlations between female and male strobilus production in all seed orchards. The status numbers (N-s) were calculated as 19.3 (64% of census number) and 23.2 (66%) in two R brutia seed orchards, 29.2 (94%) in a R nigra seed orchard and 25.7 (92%) in a R sylvestris seed orchard. Male fertility variation was larger than female fertility variation in R brutia and P. nigra seed orchards, while it was an opposite situation in the P. sylvestris seed orchard. The effect of fertility variation was discussed for the establishment of new seed orchards and the management of current orchards in Turkey.