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Prunus avium is primarily cultivated for its fruit, sweet cherries. However, it is also used to produce high-quality timber. In a P. avium seed orchard, gametophytic self-incompatibility is a restriction for free pollen flow and should be considered when establishing basic forest materials. In this study, S-locus diversity and cross-incompatibility of wild cherry individuals in clonal banks established for breeding for timber production were investigated. Wild cherry trees (140) with outstanding forest growth habit, collected in northern Spain, grafted and planted in two clonal banks, were genotyped at the S-locus. The self-incompatibility S-locus genes, S- RNase and SFB, were analysed by PCR. Twenty-two S-haplotypes, resulting in 72 different S-genotypes, were identified. The genotypes were grouped into 33 incompatibility groups and 39 unique genotypes. This initial S-locus analysis revealed large genetic diversity of wild cherry trees from the Spanish northern deciduous forest, and provides useful information for seed orchard design. Wild P. avium displays significantly more genetic diversity than what is detected in local cultivars, revealing a narrowing of genetic diversity during local domestication. [ABSTRACT FROM AUTHOR]