A genetic linkage map of Prunus has been constructed using an interspecific F2 population generated from self-pollinating a single F1 plant of a cross between a dwarf peach selection (54P455) and an almond cultivar (Padre). This map consists of approximately 80 markers including 10 isozymes. 12 plum genomic, 19 almond genomic and 40 peach mesocarp specific cDNA clones. The backbone map will be used for identifying the genomic locations and characterization of genes governing important economic traits in the genus Prunus. Of particular interests are those genes associated with fruit ripening and mesocarp development in peach and almond.