The name troglodytes means "hole dweller", and is a reference to the bird's tendency to disappear into crevices when hunting insects or to seek shelter.

It was formerly considered to be conspecific with the northern house wren (Troglodytes aedon).

The southern house wren was formally described in 1823 by the German naturalist Johann Andreas Naumann under the binomial name Troglodytes musculus.

He specified the type locality as the state of Bahia in eastern Brazil.

[7][8][9] Twenty-one subspecies are recognised:[8] In Argentina, southern house wrens dispersed more frequently between-seasons than within a season, with females dispersing more often than males.