The neotropical physaloid genera Witheringia and Brachistus have long been subject to taxonomic confusion.  We obtained tissue from well-documented species of these genera, including multiple accessions from widespread taxa, to generate a molecular systematic framework. We present Bayesian phylogenies based on sequences of one chloroplast (trnL-trnF) and two nuclear loci (ITS and waxy).  The major findings are that: 1) Witheringia and Brachistus together form a well-supported monophyletic group, 2) Brachistus is nested within Witheringia, 3) two Mexican endemic species represent the earliest diverging lineages of the clade, 4) several proposed synonyms represent distinct species, and 5) sequenced accessions include several new species awaiting description. The four currently recognized species of Brachistus are transferred to Witheringia, necessitating the new combination Witheringia knappiae (Mont.-Castro & Sousa-Peña) Bohs, comb. nov., and Athenaea affinis C.V. Morton is lectotypified. A list is also provided for names now excluded from Brachistus and recognized as belonging to other genera.

DNA was extracted from 31 ingroup accessions, with 29 of these collected by the authors. Ingroup sequences were obtained by Sanger sequencing at three loci: ITS, waxy, and trnL-F.  Sequences for eight outgroup taxa were procured from GenBank. Sequences were aligned using Geneious and adjusted by eye.