The eastern fence lizard, Sceloporus undulatus, is a broadly distributed polytypic species. We surveyed allozyme variation with the goal of generating an intraspecific phylogeny to evaluate the current classification of the species. We electrophoretically assayed 24 loci from 12 populations of S. undulatus, which comprised 6 of the 11 recognized subspecies, 3 additional species of Sceloporus (S. occidentalis, S. virgatus, and S. woodi), and an outgroup taxon, S. clarki. Out of the 24 loci, 14 loci were variable. Phylogenetic analyses using distance, likelihood, and parsimony resulted in trees that were inconsistent with current subspecific designations. Three species of Sceloporus (S. occidentalis, S. virgatus, and S. woodi) arose within S. undulatus. Two major lineages of populations of S. undulatus were identified: (1) a midwestern grasslands group that includes the population from Missouri, and (2) various populations from the eastern woodlands and western canyonlands. The subspecies S. u. hyacithinus and S. u. undulatus are polyphyletic, whereas S. u. garmani and S. u. tristichus are paraphyletic. No fixed allele differences were observed among the populations of S. undulatus, or among the other species of Sceloporus. Our results indicate that the present subspecies designations do not portray patterns of evolutionary relatedness and require re-evaluation.