Current citrus breeding programs have three objectives: developing diverse varieties that satisfy assorted commercial needs; improving overall fruit quality; and releasing varieties quickly. However, these objectives may conflict with each other owing to the limited available orchard space, and conventional breeding systems have not progressed rapidly enough to resolve this problem. “Citrus breeding 2.0” is a novel approach to overcome the trilemma of citrus breeding. “Citrus breeding 2.0” will increase diversity by referring to parentage, improve the overall fruit quality through composite selection, and minimize the breeding time through genomics-assisted selection. Extended applications of “Citrus breeding 2.0” are also possible for purposes of rebreeding or improving an existing variety.