Fruit trees are vital components of agricultural systems worldwide, serving as sources of nutrition, income, and ecological services. They have exceptional nutritional profiles and culinary versatility. Wild relatives are the key gene pool for enhancing the resilience, productivity, and quality of cultivated fruit crops. They have exceptional genetic diversity, often surpassing that of cultivated varieties especially in characters such as pest tolerance, disease resistance, abiotic stress tolerance, and adaptation to various environmental conditions. Owing to the perennial nature, conventional breeding methods in fruit crops are cumbersome, laborious, and time-consuming. Fruit crop breeding has been revolutionized by the rapid advances in genomics and molecular biology, which have brought about novel tools such as genome editing, transgenic techniques, omics approaches, and marker-assisted breeding. The advancement of perennial crops could be greatly accelerated by these technologies. Advancements in sequencing technology enable broader exploration of the genetics and genomics of wild relatives across a more extensive array of crops. This chapter emphasized the significance of wild relatives of fruit trees and their role in fruit breeding. This review summarizes the application of sequencing, MAS, omic approaches, transgenic and genome editing in biotic and abiotic stress tolerance, and quality breeding of fruit trees.