Usnea mayrhoferi was first formally described by Maria de los Angeles Herrera-Campos, Frank Bungartz, Camille Truong, and Philippe Clerc in 2018.

The type specimen of Usnea mayrhoferi was collected by Clerc on the Sierra Negra volcano (Isabela Island) at an altitude of 913 m (2,995 ft); there it was found growing on a living fencepost in a farming area.

However, it can be distinguished by its unique combination of characteristics, including its blackened trunk, crowded soralia, and broad axis.

While some of these species share similar chemistry, Usnea mayrhoferi has only been observed with a single chemotype containing norstictic acid.

[2] This lichen bears resemblance to a group of similar and possibly closely related species, including Usnea brattiae, U. cedrosiana, U. krogiana, and U. patriciana.