[1] The family underwent a major molecular phylogenetics-led reorganisation in 2023, in which 17 genera were recognised and formally established as new or reinstated.

The Gomphillaceae has undergone significant taxonomic revision as molecular analysis techniques have improved scientists' understanding of relationships between species.

As of 2024, the family includes approximately 440 accepted species, of which 422 are lichenised (form a symbiotic relationship with algae) and 18 are lichenicolous or fungicolous (grow on other lichens or fungi).

Recent molecular phylogenetics studies (analysis of DNA sequences to determine evolutionary relationships) have led to a major reorganisation of the family's classification.

[3] The internal structure of hymenium (the fertile, spore-producing part of the lichen), called the hamathecium, consists primarily of branched and interwoven paraphyses.

The asci, or spore-producing sacs, are annelasceous and feature a distinctive apical tholus and ring structure.