Research into the plant hormone auxin has always been tightly linked with the use of small molecules. In fact, most of the known players in auxin signaling and transport in the model plant Arabidopsis thaliana were identified by screening for resistance to auxin analogues. The use of high-throughput screening technologies has since yielded many novel molecules, opening the way for the identification of new target proteins to further elucidate known pathways. Here, we give an overview of well-established and novel molecules used in auxin research and highlight the current status and future perspectives of chemical biology approaches to auxin biology.