Genome resources for apple (Malus x domestica Borkh), the main fruit crop of temperate regions, have built up over the past five years, culminating in the sequencing of the apple cultivar ‘Golden Delicious’ (GD) genome. In spite of the availability of a high-quality genome sequence, a large collection of expressed sequence tags, and a physical map, high-resolution genetic maps remain crucial resources for molecular breeding programs as well as for fine-mapping quantitative trait loci. We describe here the construction of an apple dense integrated genetic map derived from six F1 populations and, for the first time, its physical anchor to the sequenced genome of GD. Polymorphisms discovered by assembling the two haplotypes of the GD genome were used to develop markers for each metacontig to correlate them with linkage groups. The map included 1,730 polymorphic markers, 196 SSRs, 1,500 genomic-derived SNPs and 34 EST-derived SNPs. In total, 17 linkage groups were identified based on SSR markers mapping to existing apple linkage maps. All sequenced markers, well positioned on the genetic map, were used to order and to orient metacontigs along the appropriate linkage groups. In addition, marker information was used to avoid building chimerical metacontigs from different linkage groups. Many genes related to disease resistance, fruit quality, plant development, and reaction to environment have been identified and mapped to chromosomes. Region-dependent estimations of physical and recombinational distance, and correlation of recombination with specific sequence parameters are also presented.