Brown rot, caused by Moniliniaspp., is one of the most economically important diseases of stone fruits. The fungus mainly affects the blossoms and fruit, and the resulting disease can lead to significant pre- and postharvest yield losses. Estimated yearly cost to the U.S. stakeholders for chemical protection against the disease can reach $170M. Although some degree of resistance in peach landraces (‘Bolinha’) and interspecific material (almond × peach) has been reported, genetic resistance to brown rot in peaches is still lacking. In commercial peach production, the disease is managed by practicing sanitation and the application of fungicides. The Clemson University peach breeding program within the RosBREED project aims to understand the genetics behind the peach fruit response to brown rot with the ultimate goal of combining disease resistance with high fruit quality via DNA informed breeding. To this end, 26 cultivars /advanced selections and 138 progeny, representing 9 breeding families, with ‘Bolinha’ source of resistance have been phenotyped for fruit response to brown rot using wounded and non-wounded disease assays in 2015 and 2016. Previously obtained genotypic data, and reported QTLs associated with brown rot response in peach fruit, were used to obtain preliminary information on variability in brown rot associated genomic regions. Phenotypic performance or trait values of these alleles/ haplotypes were discussed. The data presented here provide a foundation for developing predictive DNA information that has potential for immediate application in U.S. peach breeding.