The superorder Archonta has been hypothesized to include primates, tree shrews, bats, and flying lemurs as descendants of a common ancestor. More recently, a diphyletic origin for bats has been proposed. To evaluate these hypotheses, the nucleotide sequence of the mitochondrial cytochrome oxidase subunit II gene was determined from a bushbaby (Galago senegalensis), flying lemur (Cynocephalus variegatus), tree shrew (Tupaia glis), spear-nosed bat (Phyllostomus hastatus), rousette bat (Rousettus leschenaulti), and nine-banded armadillo (Dasypus novemcinctus) and was compared with published sequences of a human, cow, and mouse. Phylogenetic analyses of the sequences give evidence that primates, tree shrews, and flying lemurs have a recent common ancestor but that bats are genealogically distant. The monophyletic origin of bats is supported. Contrary to interpretations based on morphological data, tree shrews are shown to be no more closely affiliated with primates than are flying lemurs. Analyses of the cytochrome oxidase subunit II gene give marginally more support to a Dermoptera-Scandentia clade than to a Dermoptera-Primates clade.