Sustainability of fruit production worldwide is heavily dependent on advances in fruit genetics. Changing environments, innovative production systems, increased pest and pathogen pressure and fluctuating consumer preferences are forcing fruit producers to adjust at a higher pace than ever before. This chapter provides an overview of the advances in fruit genetics as they pertain to discoveries in fruit quality and disease resistance, and their application to the improvement of fruit production and sustainability. The chapter looks at developments in genomic mapping, marker-assisted breeding and biotechnology. The chapter also examines the genetics of fruit quality and disease resistance, and includes a detailed case study on hot spot on chromosome 4 in Prunus. Finally, the chapter looks ahead to future research trends in this area and suggests further reading on the subject.