Reporter genes have been widely used in plant molecular biology, typically to discern patterns of gene expression, but also as markers of transformed cells during stable transformation procedures. The ideal marker gene would be expected to display characteristics such as ease and cheapness of use, lack of toxicity, and robustness; and the most commonly used ones – GUS, GFP, LUC, and C1 + R/B– (anthocyanin accumulation) exhibit most if not all of these properties. Each, however, differs in potentially important ways, and before deciding which to use it is important to consider carefully your particular set of experiments and the plant tissue you will be using. In this chapter, I will introduce each marker, outline protocols for their use, and discuss their strengths and weaknesses.