The citrus gene pool displays a huge diversity for useful traits such as fruit quality, resistance to diseases and abiotic stress adaptation. Efficient exploitation of this germplasm by conventional citrus breeding requires the developments of early selection methods, particularly the one based on marker-traits association. This chapter reviews the recent developments in genetics and genomics to decipher the citrus genome and optimize its exploitation. The chapter identifies some of the specificities of the citrus gene pool and their implications in addressing the link between phenotype and molecular diversity. After a review of citrus molecular markers, the chapter describes recent important genetic and genomic developments and particularly the release of reference genetic maps and genome sequences and phylogenomic studies based on whole genome resequencing and GBS data. The chapter then discusses efforts to link phenotypic and molecular variability and concrete applications of marker assisted selection presented. Finally, the chapter looks ahead to future research trends in this field.