Phacopsis species appear as partially immersed, shiny brown to black apothecia that cause gall-like deformations on the thallus of the host lichen.

Features of Phacopsis used to distinguish species from each other include the shape of their spores, and the colour and reaction of the hypothecium (a tissue layer under the spore-bearing hymenium) when stained using an iodine–starch test.

Phacopsis was circumscribed by French mycologist Edmond Tulasne in 1852 with multiple species originally classified in genus Abrothallus.

[3] Of the other two species originally included in Phacopsis by Tulasne, P. clemens has since been referred to the genus Arthonia,[4] while P. varia is now known as Opegrapha physciaria.

[5] In 1988, Dagmar Triebel and Gerhard Rambold proposed that Phacopsis should be considered synonymous with Nesolechia (another genus of lichenicolous fungi in the Parmeliaceae), owing to similarities both in the structure of their apothecia and the characteristics of their hymenia.

[6] This proposed synonymy, however, was not accepted by several authors in the years following,[7][8][9] until 1995 when Triebel, Rambold, and John Elix showed that the supposed differences that separated the two genera were not consistent.

[10] Following this, Ove Eriksson and David L. Hawksworth used an expanded generic concept of Phacopsis (sensu lato) in the next update of their regular publication on ascomycete systematics, Systema Ascomycetum.

[12] In 2017, Divakar and colleagues used a then-recently developed "temporal phylogenetic" approach in an attempt to make family- and genus-level classification more consistent with evolutionary history.

[14] In a 2018 review of taxonomic developments in the family Parmeliaceae, the authors recommended not synonymizing Nesolechia and Phacopsis, suggesting that the separation between these two genera has not yet been sufficiently established.

[17] Using electron microscopy, Josef Hafellner examined the asci (spore-bearing cells) of the type species P. vulpina, showing them to be similar to those commonly found in members of the Lecanoraceae, and so he considered the genus most appropriately classified in this family.

In 2002, André Aptroot and Triebel suggested a possible close phylogenetic relationship between Paraparmelia and Xanthoparmelia, since Phacopsis australis was noted to grow on representatives from both of those lichen genera.