The Snake River pilose crayfish Pacifastacus connectens and pilose crayfish Pacifastacus gambelii are sister species endemic to western North America that require increased conservation attention due to apparent range declines. We report results of molecular analyses that sought to clarify where P. connectens and P. gambelii occur relative to each other as well as morphological analyses that sought to help nonspecialists reliably identify these species in the field. We conducted our analyses on voucher specimens recently collected from across the presumed native ranges of both pilose crayfish species. We sequenced the mitochondrial cytochrome c oxidase subunit I gene of these crayfish specimens and then built Bayesian and maximum likelihood phylogenetic trees on these sequence data. Next, we made a series of morphological measurements on crayfish specimens, which we analyzed as morphological ratios in a principal component analysis. We found that P. connectens represents a diverse polytomy of multiple lineages distributed in the middle Snake River watershed and adjacent Harney Basin, whereas P. gambelii represents a monophyletic lineage of extremely low genetic diversity distributed primarily in the upper Snake River watershed and adjacent Bonneville Basin. We also confirmed that the pilose crayfishes are morphologically distinct relative to each other, with P. connectens reliably possessing a narrow or acute rostrum and P. gambelii reliably possessing a broad or obtuse rostrum. Alternatively, some other morphological characters historically associated with the 2 pilose crayfish species were less reliable in differentiating P. connectens and P. gambelii. Our findings should help natural resource managers, like fisheries biologists, anticipate where the pilose crayfishes occur and identify them under field conditions. Future investigations into the taxonomic status and phylogenetic relationships between these crayfish species would benefit from high-throughput sequencing focused on the nuclear genome.