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The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases such as psoriasis and inflammatory bowel disease. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation mediated by CCL20. Here, we present two inactive CCR6 structures determined by cryo-EM in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. OXM1 and OXM2 are oxomorpholine (OXM) analogues which are highly selective for CCR6 and disrupt the molecular network critical for receptor activation by binding to an extracellular allosteric pocket within the transmembrane domain. A U-shaped conformation stabilized by intramolecular interactions was revealed by structural and NMR studies of active OXM analogues. SQA1 is a squaramide (SQA) derivative with close-in analogues that were previously reported to be antagonists of CCR6 and other chemokine receptors. Our structures reveal an intracellular pocket occupied by SQA1 that overlaps with the G protein binding site. In addition, SQA1 stabilizes a closed conformation of the intracellular pocket, a hallmark of the inactive state of GPCRs. Minimal communication was found between the two allosteric pockets. Overall, our work provides new evidence of the versatility of GPCR antagonism by small molecules, complementing previous knowledge on CCR6 activation, and sheds light on drug discovery approaches to target CCR6 for autoimmune disorders.