Chaenotheca was established as a genus by
Theodor Magnus Fries in 1860, but several of its species had already been treated earlier under a broader concept of
Calicium by
Erik Acharius (1816). Fries separated
Chaenotheca from related calicioid lichens on the basis of a
crustose thallus and stalked apothecia with a distinct , together with simple, pigmented, spherical spores. He also rejected the then-common practice of placing these species in "
Cyphelium" as an inappropriate application of that name. The genus concept was soon widely adopted, and it was later fixed by
lectotypification with
Chaenotheca trichialis by
Clements and
Shear (1931). In parallel, Fries and subsequent authors continued to recognise
Coniocybe as a closely similar genus, traditionally separated by its more weakly developed excipulum. More recent work has left the phylogenetic position of
Chaenotheca unsettled: no close relative has been firmly identified for the genus or for the family Coniocybaceae, and both morphological and preliminary molecular evidence suggest it does not belong in the
Lecanorales. In the same study, the main molecular groupings broadly matched clusters previously suggested from morphology and chemistry, but the deeper branches of the tree were weakly supported, making it impossible to determine from the
internal transcribed spacer (ITS) data alone whether the two subgenera each form natural, exclusively related groups. '' A specialized
lineage of mazaediate (producing a powdery spore mass at maturity) lichens living on the fruit bodies (sporocarps) of the polypore genus
Trichaptum was long treated within
Chaenotheca. Early records include a
Trichaptum-inhabiting variant mentioned by Fries in 1865, and a North American taxon described as
Calicium obscurum in 1909 (later treated as
Chaenotheca obscura); the name
Chaenotheca balsamconensis was introduced much later for the same entity. Multi-locus phylogenetic analyses support these
Trichaptum specialists as a distinct lineage within Coniocybomycetes, sister to the combined clade of
Chaenotheca s. lat. and
Sclerophora, and they have been separated as the genus
Chaenotricha with
Chaenotricha obscura as the type species and
Chaenotricha cilians described as a second species.
Cybebe was described as a
monospecific genus for
Cybebe gracilenta, separated from
Chaenotheca mainly by its unusual
ascus development (with asci formed in chains) and its unpigmented spore wall; however, molecular analyses place
C. gracilenta well within
Chaenotheca, forming a strongly supported clade with
Chaenotheca gracillima. The characters used to define
Cybebe are therefore best interpreted as derived features of that
lineage (specialised features that evolved within that branch rather than being inherited from a common ancestor), and
Cybebe is treated as a
synonym of
Chaenotheca. ==Fossil record==