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The plant hormone, auxin plays a crucial role in many aspects of plant development. Endogenous auxin action was modulated at three steps, auxin metabolism, transport and signaling. Indole 3-acetic acid is major naturally occurring auxin. It has been major issue how this simple molecule elicits profound responses on plant development. Forward and reverse molecular genetics approach using a model plant Arabidopsis have identified fundamental components of auxin signaling and transport, and illustrated the molecular mechanism of auxin action. However, it is still hard to study the physiological role of auxin beyond the model plants. To complement the molecular genetic approach to auxin biology, we have been investigated the chemical probes on auxin signaling and transport. Because chemical probe can potentially overcome the functional redundancy of cognate target proteins and accomplish the regulation of orthologue protein function beyond a species. We have identified auxin signaling inhibitors, yokonolide B and terfestain A by a forward screen of microbial extracts using a transgenic auxin-inducible reporter line. Structure-based drug design approach for auxin analogs identified auxin antagonist specific for TIR1/AFB auxin receptors. We recently developed chemical tools for auxin polar transport, such as caged auxins and competitive auxin transport inhibitors. Our work substantiates the useful chemical tools for plant biology.