Central Europe can be taken as a geographical and historical link between the western growing countries and Asian gene centres of tree fruits and hence information on the genetics of local cultivars might be very interesting from a crop evolutionary perspective, besides its economical importance. Our long-term study is being carried out to S-genotype stone fruit (mainly almond, plum, sweet cherry and apricot) cultivars and landraces. A complete S-genotype was determined for 20, 11, 47 and 120 cultivars and selections of almond, Japanese plum, sweet cherry and apricot, respectively. Among Eastern European almond cultivars, two novel crossincompatibility groups (CIGs) were identified and allele-specific PCR was developed to discriminate between alleles with matching intron sizes. Our results with Japanese plum clarified and harmonized two different allele nomenclatures. One CIG has been established and a table was assembled including 49 cultivars assigned to I-VII CIGs. In apricot, a total of 13 new S-alleles were identified from Eastern European and Asian accessions. Many Turkish cultivars were classified into new CIGs, III-XIV, which was surprising as apricot has been known traditionally as a mainly self-compatible (SC) species in Europe. Results suggest that the mutation rendering apricot SC might have occurred somewhere east from Central Turkey. Connections between Hungarian and Turkish germplasm were confirmed. In sweet cherry, new alleles have been identified and characterized from Turkish cultivars and selections. Wild cherry alleles were abundant in the S-locus of such selections. Our results give information on S-allele diversity from regions between the main cultivation countries and the gene centres of stone fruits. The increased number of the S-alleles present in tree fruit cultivars native to the regions from Eastern Europe to Central Asia holds considerable implications in relation to the S-genotyping methods, cultivation and breeding strategies as well as crop evolution.