Northern bog-lemmings, Mictomys (Synaptomys) borealis, Richardson 1828, are currently being assessed for federal protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a persistent deficiency of data reflecting the biological attributes of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5,939 and 11,513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog-lemmings.