The progress of the European Apple Genome Mapping Project will be described. Five populations segregating for a range of agronomic genes have been established in six European countries. Isozyme systems, RFLPs, RAPDs, and other PCR-based markers are being used to construct a unified genetic linkage map. Genotypic and phenotypic measurements have been precisely defined and standardized among participants. Phenotypic measurements for many agronomic traits are being replicated in different geographical locations over several years. Statistical and genetic analyses are aimed at defining components of genetic variation that account for “genes” manipulated by apple breeders. The segregation of fungal and insect resistance genes, tree habit, juvenility, budbreak, and many fruit characters has been scored. Markers have been identified linked to and flanking scab and mildew resistance genes. RAPD markers have been converted to codominant PCR-based markers for selection purposes. The JoinMap program has been extended for linkage analysis of crosses between heterozygous parents. A method for mapping QTLs in outcrossing species has been developed, together with software that is able to contend with dominant markers and missing data. Associated research is being carried out on the genetics and diversity of fungal resistance genes, fruit quality, and the socioeconomic aspects of apple production. The relational database, APPLE-STORE, has been designed and implemented for combined management of agronomic and genetic information. Synteny of linkage groups between Malus and Prunus has been established.