It belongs to the genus Verrucaria, a group of lichens characterised by their small, flask-shaped fruiting bodies (perithecia) and crustose growth form.

DNA analysis of the internal transcribed spacer region shows a sequence divergence of 4.5–6.8% from its closest relatives, supporting its status as a separate species.

[2] The perithecia are small to medium-sized (0.15–0.47 mm in diameter) and partially immersed in the rock substrate, usually leaving shallow to fairly deep pits.

[2] A key diagnostic feature of V. vacillans, reflected in its species epithet, is its highly variable involucrellum (the outer layer covering the perithecium).

The involucrellum can range from apical (covering only the top) to reaching the base of the perithecium, and its thickness and orientation relative to the exciple (inner layer) are also variable.