Breeding for fruit quality improvement is critical for sustaining consumer interest and providing long-term profitability for the apple industry. Priority breeding targets consist of eating quality, appearance, and storability traits (to ensure year-round availability of fruit). Apple breeding is a resource-intensive process constrained by its heterozygosity and long generation time. Advancements in genomic research and DNA technologies are increasing our knowledge of genomic regions and diagnostic markers linked to priority traits. This chapter describes breeding for quality improvement, address challenges of phenotyping, and provide a comprehensive review of DNA markers associated with fruit quality traits.