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In this study, the complete mitochondrial genome sequence of click beetle Agriotes hirayamai (GenBank accession no. MG728108) was obtained using next-generation sequencing (NGS) method. The complete mitochondrial genome of A. hirayamai is 16,156 bp in length and contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and a control region. The gene arrangement is consistent with the typical insect mitochondrial genome. Maximum likelihood tree shows that the newly sequenced A. hirayamai cluster with other two sampled species of Agriotes and the family Elateridae is monophyletic.