Mitochondrial DNA sequences were used to determine the phylogenetic relationships of the Lampropeltis mexicana complex to other taxa of the Lampropeltis genus. Several major nodes were consistently recovered, though the relationships of these nodes to each other was not fully resolved. Results revealed two polyphyletic clades with taxa from the mexicana and triangulum groups in both clades, referred to as a "northern" and a "southern" clade. There was very little sequence divergence among taxa of the northern clade. The concept of reticulate evolution and the genealogical species concept were used to interpret the historical biogeography of these two groups. During the eastward radiation of these two groups from a common ancestor on the Mexican Plateau, a geographic bottleneck in the Sierra Madre Oriental may have induced gene flow between the two groups and subsequent lineage sorting may have occurred.
Additionally, contact between these two groups in southern refugia during Pleistocene glaciations may have again resulted in gene flow. This possibility, combined with the strong morphological and ecological differences between the mexicana and triangulum groups, suggests the gene trees derived from the mtDNA analyses in this study may not be congruent with the species tree that represents the true evolutionary history of these two groups.