On the basis of plumage coloration and mitochondrial DNA variation, four main groups are recognized within the Fox Sparrow (Passerella iliaca): the red group (iliaca, RE), sooty group (unalaschcensis, SO), thick-billed (megarhyncha, TB), and slate-colored (schistacea, SC). To establish phylogenetic relationships among those four groups, we analyzed 2119 base pairs of sequence from four mitochondrial regions: ND2, ND3, cytochrome b, and control region. The control region is less variable than the coding genes surveyed. Both maximum parsimony and maximum likelihood resolved the same ingroup relationships (RE(SC(TB,SO))). However, placement of the root could not be established, even with four outgroups. Lack of resolution of the root is due to the nearest living relative of the Fox Sparrow being over 11% divergent. Despite lacking a clear root, the data suggest that the two taxa connected by a hybrid zone (TB, SC) are not sister species, which has implications for species limits because under the biological species concept they should be lumped. We recommend that all four main groups be recognized as species.