Abstract Accurate species delimitation is critical to identifying the conservation status of species. Molecular species delimitation methods have revealed previously unrecognized cryptic species across the taxonomic spectrum. However, studies vary in the molecular markers selected, analytical approaches used, and taxon sampling, which sometimes results in conflicting conclusions. One example of such a conflict is seen in the species delimitation analyses of the western bumble bee, Bombus occidentalis. This species was once an abundant insect pollinator in western North America but has declined severely since the mid 1990s and is predicted to continue to diminish under even optimistic future climate scenarios. Complicating this conservation crisis, the species status of B. occidentalis has varied over time, with most recent studies recognizing one or two species. Previous studies that used molecular methods to address this question focused on a Bayesian phylogeny of the mitochondrial cytochrome oxidase I (COI) gene. Phylogenetic studies that focus on a single gene are criticized for misrepresenting the evolutionary history of species because nuclear and mitochondrial genomes, and even some genes within them, may have different evolutionary patterns. We tested a two species hypothesis of the B. occidentalis complex using nuclear (ultraconserved elements) and mitochondrial (COI) markers to infer maximum likelihood and Bayesian phylogenies for the taxa. We present our results and conclusions from eight species delimitation methods. Based on the genomic, morphological and geographic differences between the taxa we find support for the two species hypothesis, with B. occidentalis and B. mckayi as separate species. We discuss the strengths and limitations of each genetic dataset and delimitation method, make recommendations for best practices, and highlight opportunities for equitable knowledge and technology development for phylogenomics in conservation biology.