The FLP/FRT site-specific recombination system of Saccharomyces cerevisiae was expressed in stably transformed tobacco plants. The FLP protein efficiently catalyzes recombination between two directly repeated FLP recombination target (FRT) sites, deleting the sequence between them. In the constructs tested here, this deletion places the CaMV 35S promoter adjacent to a hygromycin resistance marker; transcriptional activation of the marker allows direct selection of recombination events. After crossing plants containing an integrated FLP expression construct with plants containing a FLP substrate, F1 seedlings can be selected directly for hygromycin resistance, indicating that recombination occurs at, or very early after zygote formation. Molecular analysis confirmed the expected recombination product.