The beginning of the modern transcriptomics era in Prunus spp. might be traced back to the fi rst report describing expressed sequence tag (EST) production from peach, dating back to year 2000 (Hayama et al. 2000), when about 200 sequences were described, obtained from libraries constructed from RNA of three different fruit developmental stages. Besides EST production, several differential display approaches in different species have been undertaken with peach (P. persica) being investigated primarily. By the time that this chapter has been written, the whole peach genome sequence was available (Sosinski et al. 2010) as the main achievement of the activities of several laboratories that in the last decade faced genomics in order to expand the molecular tools needed to tackle the many biological questions underneath the agronomical traits in the Prunus genus.