Citrus is one of the most important fruit crops worldwide. Cultivar development programs, however, have had little impact because of impediments associated with reproductive biology, and the lack of cost- effective selection strategies. Genome characterization and mapping projects with Citrus and related genera have provided information that will be of great practical value to breeding programs immediately, and that will enable more precise genetic dissection and manipulation of important characteristics in the near future. Markers have been developed that can be utilized for indirect selection of desirable hybrids for resistance to citrus tristeza virus (CTV) and citrus nematode (Tylenchulus semipenetrans), for dwarfing, and for a gene that influences fruit acid accumulation. Work is in progress to map genes for resistance to Phytophthora and iron chlorosis, as well as QTLs for tolerance of salinity and cold temperatures. Other objectives that are being addressed include fine-resolution mapping of the CTV resistance gene region and development of allele-specific markers for CTV resistance (to enable map-based gene cloning), identification of sequences that influence DNA methylation, and the evaluation of SSR-anchored PCR markers. Good collaboration among scientists in Florida and California will ensure timely exploitation of information and methods by citrus breeding programs, and will enable molecular genetic manipulation of important traits in the near future.