The millipede genus Brachoria consists of 29 species and occurs predominately in the Valley and Ridge Province of the Appalachian Mountains. Species in this genus are aposematically colored indicating to predators that they have defense secretions comprising hydrogen cyanide. The level of endemic biodiversity and variability of warning coloration make this group ideal for the exploration and study of mimicry evolution. Brachoria species appear to mimic several closely related genera and one of several models (Batesian, Müllerian, or quasi-Batesian) may be consistent with mimicry in this genus. As a prelude to a forthcoming revision of Brachoria and an inquiry into mimicry evolution of the genus, we used a total evidence exemplar phylogeny to infer the evolutionary history of its species within the higher-level taxon Apheloriini. We found that Brachoria species comprise two polyphyletic lineages. We discuss the utility of multiple datasets and methods in phylogenetic inference, and explore hypotheses related to higher taxon composition and mimicry evolution.