In this review, the use of the most common selection marker genes on plant transformation and the effects of their respective selective agents are discussed. These genes could be divided in two categories according their mode of action: genes for positive and negative selection. The retention of the marker gene flow through chloroplast transformation is also discussed. Further, strategies to recover marker-free transgenic plants, involving multi-auto-transformation (MAT), co-transformation, site-specific recombination and intragenomic relocation of transgenes through transposable elements are reviewed.