Peach [Prunus persica (L.) Batsch] belongs to the Prunus genus, member of the Rosaceae family. The Prunus genus, within the subfamily Prunoideae, is characterized by species that produce drupes as fruit (also referred to as stone fruits), and contains a significant number of agriculturally important fruit tree species [i.e., almond (Prunus dulcis Mill.), apricot (Prunus armeniaca Linn.), sweet cherry (Prunus avium L.) and sour cherry (Prunus cerasus L.), and plum (Prunus japonica and Prunus domestica)]. Several other species like myrobalan plum (Prunus cerasifera Ehrh.) or Sainte Lucie cherry (Prunus mahaleb L.) are mainly used as Prunus rootstocks. Although Prunus is an economically and biologically important genus, little was known about the genome structure and organization until the breakthrough of DNA marker technologies. Peach has distinct advantages that make it suitable as a model species for comparative and functional genomics. It has a short juvenile phase (2–3 years) compared to many other tree species, and a small genome: 5.9×108 bp or 0.61 pg/diploid nucleus (Baird et al. 1994). This is only about twice the genome size of Arabidopsis thaliana (Arumuganathan and Earle 1991). All the Prunus species have a base chromosome number of x=8. Peach, almond, sweet cherry and myrobalan plum have a diploid genome (2n=2x=16), whereas sour cherry is tetraploid (2n=4x=32) and European plum hexaploid (2n=6x=48). Moreover, peach is genetically the bestcharacterized Prunus species with a fair number of genes controlling important traits and having a Mendelian behavior (Hesse 1975; Monet et al. 1996; Table 1). For all these reasons, peach was chosen as a model for Rosaceae and a physical map has been initiated.