It was formerly considered conspecific with the American red squirrel (T. hudsonicus), but a 2016 study found sufficient phylogenetic evidence indicating it was a distinct species.

In addition, genetic sampling indicates that squirrels from the Sacramento Mountains of New Mexico form a highly divergent clade that dates back to the Last Glacial Maximum, about 130,000 years ago.

Squirrels in the San Mateo Mountains also appear to be genetically divergent, although this is only based on a single individual.

If this lack of connectivity is compounded with further degradation of their habitats, the population dynamics of this species could eventually be driven by extinction.

One notable subspecies, the Mount Graham red squirrel, is already thought to be endangered.