Characterization of the Complete Mitogenome of Polypedates braueri (Anura, Rhacophoridae, Polypedates) and Insights into the Phylogenetic Relationships of Rhacophoridae

White-lipped tree frogs, <i>Polypedates braueri</i>, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of <i>P. braueri</i>. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of <i>P. braueri</i> has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of <i>P. braueri</i> and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of <i>P. braueri</i> was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (<i>O_L</i>), and two control regions (<i>CR</i>). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (-0.039) and GC-skew (-0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of <i>P. braueri</i> was closely related to that of <i>Polypedates megacephalus</i> and <i>Polypedates leucomystax</i>. Additionally, selective pressure analysis suggested that <i>COX1</i> and <i>ND1</i> were highly efficient for discriminating closely related species in the genus <i>Polypedates</i>, while <i>ND4L</i> was the most appropriate marker for population-level genetic analyses. The diversification of the <i>Polypedates</i> commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on <i>P. braueri</i> and new insights into the phylogenetic relationships of Rhacophoridae.