The primary threat to cranberry production in the northeast is losses due to fruit rot in the field. The problem is increasing in other parts of the U.S., exacerbated by climate warming trends. Even with well-timed fungicide regimes, fruit rot incidence losses continue to reach 25% or more. Fruit rot is caused by a complex of pathogenic fungi from several genera. We have identified four distinct sources of broad-spectrum resistance from our germplasm collection. Crosses to pyramid putative resistance genes in horticulturally elite genetic backgrounds have resulted in populations segregating for fruit rot resistance and higher productivity. Utilizing our 3rd generation genome assembly and genotyping by sequencing (GBS), we have identified nine quantitative trait loci (QTL) associated with resistance. QTL for other key traits have also been mapped, e.g., yield. Research continues to validate the QTL in advanced breeding populations and marker development for marker-assisted selection. The mechanism(s) of fruit rot resistance is also being explored.