This chapter provides a case of genus Polytremis Mabille, 1904 (Lepidoptera: Hesperiidae), to explain the molecular phylogeny and taxonomy of Lepidoptera and the influence of Wolbachia infection. Earlier studies of Lepidoptera were focused mainly on the morphological classification, population distribution, and identification of new species. As the supplementary to morphological research, analysis of DNA has been widely used in the phylogenetic studies of Lepidoptera. The study provides a conservative estimate that the Wolbachia infection rate in Polytremis nascens Leech (1893) is 31%, and no significant difference in the prevalence is found between the sexes. The Wolbachia infection mainly prevails in populations of P. nascens in southern China, which influence the diversity of mtDNA in P. nascens by a Wolbachia-induced sweep. The Wolbachia infection rate in Polytremis fukia Evans (1940) is 47% and shows a weak association existed between mitochondrial DNA haplotypes and wFuk1 infection status.