||Burbrink (2001) used cytochrome b sequences to examine phylogenetic relationships among E. guttata populations (one specimen from each of 53 locations throughout most of the range). He found no support for recognition of the nominal subspecies intermontanus and meahllmorum as distinct taxa; these appear to be junior synonyms of E. guttata emoryi. Burbrink identified three partitions of E. guttata: an eastern partition (east of the Mississippi River) corresponding to E. guttata guttata, a western partition corresponding to E. guttata emoryi (including E. g. intermontanus and E. g. meahllmorum), and a central partition in western Louisiana and eastern Texas. The central partition, in pine and pine-hardwood habitat west of the Mississippi River, clustered closer to the eastern partition than to the western partition. Burbrink recognized the three partitions as species using evolutionary species criteria: (1) Elaphe guttata (Red Corn Snake) (eastern partition ), (2) Elaphe emoryi (Great Plains Rat Snake) (western partition), and (3) Elaphe slowinskii (Slowinski's Corn Snake) (central partition). One specimen (Hidalgo County, Texas) of the central partition (based on cytochrome b characteristics) was located outside the presumed geographic area and habitat identified for other members of that partition. Crother et al. (2003) adopted these changes. Ernst and Ernst (2003) recognized E. emoryi and E. guttata as distinct species, but their manuscript evidently was completed before Burbrink's paper was published; they did not comment on E. slowinskii.
Utiger et al. (2002) examined mtDNA variation in New World and Old World "Elaphe" and determined that North American rat snakes included in the genus Elaphe form a monophyletic lineage that is distinct from Old World snakes that also have been regarded as Elaphe. They resurrected the genus Pantherophis for the rat snakes north of Mexico, including the following species: Pantherophis obsoletus (and P. alleghaniensis and P. spiloides, if one recognizes those taxa as species), P. guttatus, P. emoryi, P. vulpinus, P. gloydi, and P. bairdi. Crother et al. (2003) noted this proposal but did not adopt it, pending further review. Burbrink and Lawson (2007) agreed with Utiger et al. (2002) that these species do not belong in Elaphe, but suggested that the genus Pantherophis might belong in Pituophis. We retain this species in Pantherophis, following Utiger et al. (2002) pending further information on the relationships of these taxa.