| Summary: | Mitochondrial genomics, as a useful marker for phylogenetics and systematics of organisms, are important for molecular biology studies. The phylogenetic relationships of the <i>Polypedilum</i> generic complex remains controversial, due to lack taxonomy and molecular information. In this study, we newly sequenced mitogenomes of 14 species of the <i>Polypedilum</i> generic complex. Coupled with three recently published sequences, we analyzed the nucleotide composition, sequence length, and evolutionary rate of this generic complex. The control region showed the highest AT content. The evolution rate of protein coding genes was as follows: <i>ATP8</i> > <i>ND6</i> > <i>ND5</i> > <i>ND3</i> > <i>ND2</i> > <i>ND4L</i> > <i>ND4</i> > <i>COX1</i> > <i>ND1</i> > <i>CYTB</i> > <i>APT6</i> > <i>COX2</i> > <i>COX3</i>. We reconstructed the phylogenetic relationships among the genera within the <i>Polypedilum</i> generic complex based on 19 mitochondrial genomes (seventeen ingroups and two outgroups), using Bayesian Inference (BI) and Maximum Likelihood (ML) methods for all databases. Phylogenetic analysis of 19 mitochondrial genomes demonstrated that the <i>Endochironomus</i> + <i>Synendotendipes</i> was sister to <i>Phaenopsectra</i> + <i>Sergentia</i>.
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