An Agrobacterium-mediated transformation system was developed for the ornamental cherry species Prunus incisa. This system uses both an antibiotic resistance gene (NPTII) and a visible selectable marker, the green fluorescent protein (GFP), to select plants. Cells from leaf and root explants were transformed with a NPTII/GFP fusion gene, and selected visually using fluorescence microscopy. Transformed cells were then induced to undergo embryogenesis and reselected by growing on media containing kanamycin. The presence of the GFP/NPTII fusion gene in all parts of transgenic plants grown in the greenhouse for one year was confirmed by PCR and Southern blot analysis. This transformation and selection system will be useful in future work to introduce genes for pathogen resistance and ornamental traits into flowering cherry germplasm.