Candidate gene (CG) analysis can be an efficient approach for identifying genes controlling important traits in fruit production. Three chronological steps have been described for determining candidate genes for a trait—proposing, screening, and validating—and we have applied these to the problem of internal breakdown of peach and nectarine. Internal breakdown (IB), also known as chilling injury, is the collective term for various disorders that occur during prolonged cold storage and/or after subsequent ripening of stone fruit. Symptoms include mealiness, browning, and bleeding. Candidate genes for IB symptoms were proposed based on knowledge of the biochemical or physiological pathways leading to phenotypic expression of the traits. Gene sequences for proposed CGs were obtained primarily from the Genome Database for Rosaceae. Screening the CGs involved identifying polymorphism within a progeny population, relying mainly on simple PCR tests. Several polymorphic CGs were located on a peach linkage map and compared with phenotypic variation for IB susceptibility. A major QTL for mealiness coincided with the Freestone-Melting flesh locus, which itself is likely to be controlled by a CG encoding endopolygalacturonase, an enzyme involved in pectin degradation. Further gene sequences positioned on the consensus linkage map of Prunus by other researchers were co-located with QTLs for IB traits. Validation of the role of identified CGs will require detailed physiological or transgenic studies.