The two subspecies of Prairie Warblers (Dendroica discolor) differ in migratory behavior and habitat use. A concurrent study of mitochondrial DNA variation showed that behavioral differences between subspecies may persist because little gene flow occurs between subspecies. To determine whether geographic variation in morphology parallels variation in migratory behavior and mitochondrial DNA, I used measurements of museum specimens from throughout the Prairie Warbler's range. The subspecies differ in overall body size, with birds of the Florida subspecies (D. d. paludicola) significantly larger than the nominate race. Males of the subspecies differ in the extent of white coloration in the outer rectrices. These differences were apparent even among specimens collected in northern Florida and southern Georgia, where the subspecies' ranges are most proximate. Morphological differences coincide with differences in behavior and mitochondrial DNA and support the recognition of migratory and non-migratory forms of Prairie Warblers as subspecies and as potentially independent evolutionary lineages.