Removal of marker genes improves the design of transgenic plants. Homologous recombination between direct repeats provides a simple method for excising marker genes after transgenic cells and shoots have been isolated. Efficient implementation of the method requires high rates of homologous recombination relative to illegitimate recombination pathways. The procedure works well in plastids where homologous recombination predominates. Marker genes are flanked by engineered direct repeats. The number and length of direct repeats flanking a marker gene influence excision rate. Excision is automatic and loss of the marker gene is controlled by selection alone. After transgenic cells have been isolated selection is removed allowing loss of the marker gene. Excision is a unidirectional process resulting in the rapid accumulation of high levels of marker-free plastid genomes. Cytoplasmic sorting of marker-free plastids from marker-containing plastids leads to the isolation of marker free plants. Marker-free plants can be isolated following vegetative propagation or among the progeny of sexual crosses.