Endosymbionts may play an important role in the evolution of the Insecta. Bacteria such as Wolbachia, Cardinium, and Rickettsia are known to manipulate their host` reproduction to facilitate their own. Indeed, there are many well know cases where Wolbachia (Alphaproteobacteria: Rickettsiaceae) induces one of four manipulative phenotypes (cytoplasmic incompatibility, male killing, feminization, and parthenogenesis). The scale of infection among species has been a major subject of investigation, but this is not an easy endeavor and different approaches have yielded different estimates. One aspect of this problem that may be underappreciated arises when multiple yet independent samples are taken within a taxon. When independent samples within a taxon are treated as levels of a hierarchy the problem is greatly simplified because error propagates through the model in a realistic and intuitive manner. Here, we present a hierarchical Bayesian approach to estimate infection frequency where multiple independent samples were collected across multiple taxonomic levels. We apply this model to estimate the rates of infection for Wolbachia in the Lepidoptera, and apply the model with a correction to account for phylogenetic non-independence. In addition, we highlight the present body of knowledge regarding Wolbachia and its effects with regards to the Lepidoptera. Our model estimates suggests that the rate of endosymbiont infection in the order Lepidoptera is approximately 12%, which is much lower than previously estimated. Given our limited knowledge regarding the phenotypes induced by these endosymbionts, we urge caution when extrapolating the results of a positive assays.