This chapter provides an integrative review of quantitative and molecular genetic insights into donkey, mule, and hinny breeding, emphasizing the role of multi-omics in improving functional traits. It explores genomic, transcriptomic, proteomic, and epigenetic findings related to meat and milk production, skin and coat characteristics, growth performance, locomotion, fertility, and disease resistance in donkeys. Key candidate genes (e.g., LCORL, NCAPG, HOXC8, WNT7A, SCD, LEPR) and pathways underlying skeletal growth, muscle composition, fat deposition, and milk protein variation are identified, alongside breed-specific genomic signatures. Heritability estimates for functional traits such as gait, fertility, temperament, cognition, and disease resistance are discussed, providing a framework for genetic evaluations and selection indices. The chapter also examines hybrid systems (mules and hinnies), highlighting mitochondrial inheritance, sex-linked effects, and the potential of genomic tools for assessing hybrid performance despite sterility constraints. Collectively, these insights advance the application of molecular breeding strategies, marker-assisted selection, and functional genomics in equid breeding programs aimed at enhancing productivity, welfare, and adaptation.