We report here the stable expression and Mendelian segregation of transgenes in a tree species, We present physiological, biochemical, and molecular evidence for stable transgene expression of both nopaline synthase (nos) and the cotransferred gene neomycin phosphotransferase (nptII) in the flesh of apple fruit 7 years after the initial transformation, Evidence based on callus bioassays, gene expression assays, Southern blotting, and PCR data show a 1:1 segregation among 74 seedlings of the R1 progeny for the nos gene but a 3:1 segregation for the cotransferred nptII gene among a subpopulation of 47 seedlings. Southern blot data and the existence of a significant population of seedlings that possessed the nptII gene but not the nos gene have led us to propose the existence of two nptII loci and one nos locus in the original transgenic tree.