We sequenced the complete mitochondrial genome of the fishfly species Acanthacorydalis fruhstorferi van der Weele (Megaloptera: Corydalidae). The genome, which was 15,286 bp in length, included a standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a putative A+T-rich region. The gene arrangement is identical to that of most common Megaloptera mitochondrial genomes. We analyzed the preferred codon usage of the protein-coding genes and predicted the secondary structures of all the RNA transcripts. In addition, a phylogenetic tree was constructed based on the sequences of the 13 protein-coding genes, and the results supported the current view of a close relationship between Megaloptera and Neuroptera. Our analyses suggest that complete mitochondrial genome sequences are a promising method to fully resolve the phylogenetic relationships within Megaloptera.