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The complete mitochondrial genome (mitogenome) of Zemeros flegyas (Lepidoptera: Riodinidae) is 15,219 bp in length, harboring typical 37 mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an AT-rich region. The Z. flegyas mitogenome includes a cox1 gene with an atypical CGA(R) start codon and three genes (cox1, nad5, nad4) exhibiting incomplete stop codons. The putative AT-rich region is 385 bp long with several structures characteristic of lepidopteran. Phylogenetic analysis showed that Z. flegyas is closely related to other riodinids. The complete mitogenome data provided here would be useful for further understanding the higher systematics of Riodinidae.