Selectable marker genes are required to ensure the efficient genetic modification of crops. Economic incentives and safety concerns have prompted the development of several strategies (site-specific recombination, homologous recombination, transposition, and co-transformation) to eliminate these genes from the genome after they have fulfilled their purpose. Recently, chemically inducible site-specific recombinase systems have emerged as valuable tools for efficiently regulating the excision of transgenes when their expression is no longer required. The implementation of these strategies in crops and their further improvement will help to expedite widespread public acceptance of agricultural biotechnology.