Genome resources for apple (Malus×domestica Borkh), the main fruit crop of temperate regions, have been developed over the past 10 years, culminating in the sequencing of the ‘Golden Delicious’ genome. The apple genome sequence anchored to a high-density linkage map provides the apple community with new tools to identify genes and other functional elements that will enable the study of the evolution of plant genome structure, as well as facilitating genomic-assisted breeding. Transcriptomics, proteomics and metabolomics studies are greatly benefiting from the availability of an annotated genome. In this review, we report on the status of the apple genome and on current molecular and genetic tools available in apple that will improve the efficiency of the process of cultivar development; we discuss how an integrative ‘omics’ approach could greatly enhance the understanding of biological processes that determine agronomically and economically favorable phenotypes; we review the databases and bioinformatics tools that are available to manage and exploit the large amounts of biological data generated for apple and other plant genomes