The positions of over 50 SSR loci and other sequence tagged sites (STSs) have been located on the linkage maps of five apple cultivars (Rome Beauty, White Angel, Golden Delicious, Liberty, McIntosh) and two New York accessions. In most cases, the primers used produced single amplification products, permitting identification of homologous loci in the different cultivars and the precise alignment of the linkage maps generated for each. Based on this information, we present a general linkage map for apple with STS markers on each linkage group. The map consists of 17 linkage groups (equal to the haploid chromosome number for the species) with over 500 markers. The positions of several resistant gene analogues have been located on this linkage map. None of these sequences map near genes conferring resistance to scab or powdery mildew. SSR loci exhibited a tendency to cluster in certain regions of the linkage map. This clustering slightly reduces their effectiveness as genome markers for comparative mapping or germplasm diversity. However, the SSR markers definitely displayed a high level of polymorphism, making them particularly useful for genetic studies.