Bombardier beetles of the genus Brachinus Weber are notorious for their explosive defensive chemistry. Despite ongoing research on their defense mechanism, life history, and ecology, the group lacks a robust molecular-based phylogeny. In this study, three loci from mitochondrial and nuclear genomes (COI, CAD, 28S) are used to reconstruct the phylogeny of the large subgenus Neobrachinus, and test species group boundaries hypothesized by Erwin (1970) based on morphological characters. Erwin's fumans species group is found to be polyphyletic, and is herein re-defined with eight new species groups erected to reflect clades based on molecular evidence: the cinctipennis, cyanipennis, galactoderus, gebhardis, mexicanus, phaeocerus, quadripennis, and tenuicollis species groups. Erwin's cordicollis group is also expanded to include Brachinus (Neobrachinus) medius and the americanus group.