Fire blight, caused by Erwinia amylovora (Ea), is a major threat to the U.S. pome-fruit industry. Molecular markers for fire blight resistance genes are being developed to facilitate resistance gene pyramiding in the breeding of new apple rootstocks with durable fire blight resistance. Candidate fire blight resistance genes were identified by functional genomics analysis of fire blight resistant (Geneva®41) and susceptible cultivars (Malling.26 and 'Gale Gala') apple cultivars challenged with Ea. DNA markers derived from 28 candidate fire blight resistance genes were mapped in a population segregating for fire blight resistance and several co-located with two previously described quantitative trait loci for fire blight resistance. This research will facilitate introduction of marker-assisted selection to breed superior apple cultivars with fire blight resistance efficiently.