Regulatory proteins control to a large extent the expression of metabolic pathways for hydrocarbon degradation. To do so, they have evolved specific protein domains that can interact with chemical effectors, upon which they elicit their influence on the transcriptional process. In order to understand the nature of the recognition domains and the role of specific residues in effector binding, many studies have applied mutagenesis strategies. This chapter will rehearse a few strategies used for mutagenesis of regulatory proteins and screening of effector variants, followed by step-by-step protocols on site-directed and error-prone mutagenesis, and screening of mutant libraries by flow cytometry.