Species are often difficult to discern when morphological attributes do not reflect taxonomic boundaries. Cladistic analysis using individuals as OTUs allows for morphological attributes to be determined as either taxonomic characters or traits. This approach is used to review 16 taxonomic attributes that define Microphotus species. In addition, mitochondrial cyctochrome oxidase I and luciferase DNA data are analyzed for phylogenetic signal and for the potential use for species diagnosis. Analysis of morphological attributes for 317 Microphotus individuals yielded 5000 trees with poor resolution. Individuals of each species where not monophyletic thus failing to reject the hypothesis that the 16 taxonomic attributes are traits, hence they are not taxonomic characters. Separate cladistic analyses of mitochondrial COI and luciferase gene data for ten and seven OTUs, respectively, each produced one parsimonious tree. Topologies of these trees were incongruent by the placement of M. chiricahuae, M. pecosensis, and M. fragilis. Cladistic analysis of all data for 11 OTUs produced two equally parsimonious trees which were unresolved for two nodes. All data sets supported the trees, however, the luciferase data showed the most conflict with the other data sets. The data support the synonymy of M. decarthrus Fall 1912 and M. fragilis Oliver 1912 based on lack of morphological variation and geographic and temporal proximity of collection localities. Additional data is needed to make a more robust statement of Microphotus phylogeny and taxonomy.