The present invention is directed to the use of multiple site-specific recombination systems for use in transgene containment in plants. More specifically, the present invention describes coordinated excisional DNA recombination by multiple (e.g., dual) recombinases to achieve excision of unwanted transgenic DNA as well as recombinase-coding sequences themselves by self-excision. Further, the simultaneous use of multiple site-specific recombination systems in combination with controllable total sterility technology (i.e., no or reduced sexual reproduction), provides the production of environmentally safe, clean transgenic plants, enhancing the capability and public acceptance of transgenic technology for plant trait modification.