Morphological, mtCOI DNA, and luciferase DNA data are analyzed individually and simultaneously for phylogenetic signal. Analysis of 16 characters traditionally used in species identification for 317 individual Microphotus specimens yields 5000 trees with poor resolution. Although mtCOI and luciferase data conflict in basal clades, both contribute to the phylogeny of Microphotus. Based on lack of morphological variation and geographic and temporal proximity of collection localities, M. decarthrus Fall 1912 and M. fragilis Oliver 1912 are synonomized. Microphotus octarthrus Fall occurs throughout the southwestern United States in discontinuous pinyon-juniper and juniper-oak habitats. Wide geographic distribution, discontinuous habitat and limited dispersal capabilities of females makes this species ideal for the study of genetic variation. Mantel’s approximate t test indicates that populations are both geographically and genetically isolated. Twenty-six haplotypes are found among 28 individuals; haplotypes are unique for the populations studied. When subjected to a 2.3% sequence divergence rate, mean branch lengths suggest segregation of populations began in the Holocene, before Pleistocene glaciation. Although these data suggest greater species diversity, more data, including mating behavior and more genes are required to further elucidate species limits.