The results of a rangewide genetics study (mtDNA)on Crotalus horridus were reported by Clark et al. (2003). 1) The genetic differences were slight and do not warrant subspecific classification for any segment of the population. 2) The genetic breakdown is at complete odds with the morphological breakdown. Based on morphology (larger size and distinctive color pattern the southern portion of the population was formerly recognized as a subspecies, Crotalus horridus atricaudatus, the Canebrake Rattlesnake. In contrast the DNA study showed two major lineages: 1) an eastern lineage from northeast Florida northward up the Atlantic Coastal Plain and eastern edge of the Appalachians to New Jersey and New England; and 2) a western lineage from the Gulf States northward through the Appalahians and the western parts of the range to Oklahoma and north to Minnesota and Wisconsin.
How do we account for this situation? Twenty thousand years ago giant glaciers advanced across the northern part of North America. Reptiles, including Crotalus horridus died out from the northern parts of their range. Crotalus horridus survived on the southeast Atlantic Coastal Plain and adjacent continental shelf (remember that sea levels were several hundred feet lower than today) and in the lower Mississippi region with isolated populations probably suriving as far north as the karst region of northern Alabama where they managed the severe winters by overwintering in the numerousl caves and sinkholes of the region.
When the glaciers retreated these surviving populations advanced northward. They adapted to the local climates and food sources. Today there are at least five ecotypes or geographic variants, each having its own set of color morphs. These are: 1) southern (canebrake), 2) western, 3)midwestern, 4) Appalachian/eastern, 5) New Jersey Pine Barrens. None of these variants has evolved sufficiently to be considered a subspecies. (Also bear in mind that some consist of more than one lineage.) In conclusion, there are certainly geographic variants within Crotalus horridus and there is nothing wrong with referring to the southern variant as a Canebrake Rattlesnake. But they are not subspecies.
I personally believe that we need two parallel systems of classification. 1)one for the taxonomists and biogeographers, based on genetics and 2) another for the field guides based on morphology (size and color pattern). Look at the ratsnakes (the former Elaphe obsoleta group), for example. The current genetic breakdown, whether right or wrong (and it may well be correct), just doesn't work for a field guide.

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