DNA-binding proteins, including transcription factors, play essential roles in many biological processes. The identification of the DNA sequences to which these proteins bind is a first, yet still challenging, step for determining their functions. SELEX provides an excellent tool for deciphering protein DNA-binding sequence specificity, and it has been widely adopted for addressing fundamental biological questions. SELEX is an experimental procedure that involves the progressive selection, from a large combinatorial double-stranded oligonucleotide library, of DNA ligands with variable DNA-binding affinities and specificities by repeated rounds of partition and amplification. In this chapter, we describe a SELEX protocol that we have successfully applied to both plant and animal MYB transcription factors.