Among the “omic” technologies, “proteomics” and “metabolomics” are the most recently developed strategies used to describe biological systems. These technologies, when applied to the comprehensive screening of proteins and metabolites on a given cell, tissue or organ, and their comparison to the screening under different developmental or environmental conditions or in response to genetic perturbations, are useful to identify components involved in the gene-phenotype relationships. The identifi cation of these components can be applied, among others, to molecular breeding, metabolic engineering or to the elucidation of stress response pathways. When applied to fruit, these components may also help in defi ning factors involved in fruit quality, such as fl avor and color; as well as in the identifi cation of biomarkers, health promoting compounds, or factors involved in better storage conditions, all of which have important implications for better fruit management and marketing. Although “proteomics” and “metabolomics” technologies have been widely applied to different plant species and fruits since several years ago, their application to stone fruits has been just recently performed. In this chapter, a brief summary of the basics of “proteomics” and “metabolomics” are described, followed by the analysis of the results obtained when applying these technologies to stone fruits, especially peach. A broader application of these technologies to different stone fruits, as well as under different developmental or environmental situations, is needed in order to obtain larger volume of data on protein and metabolite fl uctuations that must be interpreted and integrated in a manner that could signifi cantly contribute to fruit improvement. This data integration in stone fruit, with that already obtained on transcriptome, will facilitate the construction of networks and the modeling of key processes of this fruit, which is a challenge for their application on stone fruit improvement.