The taxonomy of North American crayfishes has recently experienced a boom in interest as these crustaceans have become increasingly imperiled. Improving taxonomic resolution can inform and facilitate conservation efforts but has proven challenging for crayfishes due to the limited number of molecular tools available to resolve species complexes and delimit species. The burrowing crayfish LacunicambarusHobbs, 1969 has a particularly convoluted taxonomic history that epitomizes many of the challenges of crayfish taxonomy. Recent studies using mitochondrial DNA (mtDNA) data to resolve this genus have had mixed results: mtDNA data have successfully resolved species-clades within Lacunicambarus but have failed to resolve interspecific relationships. This has precluded research on evolutionary history and biogeography. Our goal was to resolve the phylogeny of Lacunicambarus using anchored hybrid enrichment (AHE) data, a new source of additional molecular markers for estimating phylogenetic relationships. We present the best resolved phylogeny for Lacunicambarus to date and explore discrepancies between this phylogeny and past ones based on mtDNA data. We use this new phylogeny to explore interspecific relationships within Lacunicambarus and redescribe L. erythrodactylus (Simon & Morris, 2014) and L. nebrascensis (Girard, 1852) comb. nov. Our study demonstrates the tremendous contributions that next-generation sequencing methods like AHE can make to crayfish taxonomy and conservation.