Since its description, phylogenetic affinities of the New Zealand short-tailed bat (Mystacina tuberculata) have been difficult to determine. Although previous morphological studies have aligned Mystacina with several microchiropteran families, the general consensus has been that it is nearest to Molossidae. In contrast, immunological and DNA-hybridization data support inclusion of Mystacina within the New World Noctilionoidea, although those data failed to provide resolution for relationships within the superfamily. Our purpose was to test the hypothesis that Mystacina is most closely related to Noctilionoidea rather than Molossidae and, if so, to elucidate affinities among Mystacina and other noctilionoid families. We performed a phylogenetic analysis of DNA sequences from 3 adjacent genes (12S rRNA, tRNA^Val, and 16S rRNA) in the mitochondrial genome from Mystacina and representatives of 8 microchiropteran families. Results from parsimony analysis agree with previous molecular studies that Mystacina is a member of Noctilionoidea. Additionally, this study provides resolution for relationships within the superfamily.