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The approximately 11\u2010kilobase genome is flanked by highly structured untranslated regions (UTRs), which contain various <jats:italic>cis<\/jats:italic>\u2010acting RNA elements with unique structures and functions. Moreover, local RNA elements circularize the genome non\u2010covalently through long\u2010range interactions. Interestingly, many flavivirus <jats:italic>cis<\/jats:italic>\u2010acting RNA elements contain group\u2010specific motifs or are specific for the given phylogenetic groups, suggesting their potential association with flavivirus evolution and diversification. In this review, we summarize recent advances about the structure and function of <jats:italic>cis<\/jats:italic>\u2010acting RNA elements in flavivirus genomes and highlight the potential implications for flavivirus evolution. 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