The genus was
circumscribed in 2012 by Eimy Rivas Plata,
Robert Lücking, and
H. Thorsten Lumbsch, with
Clandestinotrema clandestinum assigned as the
type species. It contains species formerly classified in the genera
Ocellularia and
Thelotrema, and corresponds to the
Ocellularia clandestina group as defined by Frisch in 2006. The genus name combines the
species epithet of the
type,
clandestina, with the
suffix -
trema.
Molecular phylogenetic analysis strongly supports
Clandestinotrema as a
monophyletic clade, which can be distinguished from other
taxa in its subfamily (Fissurinoideae) by its whitish thallus, which is often loosely corticate or ecorticate, and ocellularioid, usually , and often ascomata. In this analysis,
Clandestinotrema was divided into two
sister clades. The first
clade corresponds to species with narrow apothecial pores with an entire margin and finger-like columella, represented by the type species,
C. clandestinum. The second clade corresponds to species with broadly open apothecia with a fissured margin and broad-stump-shaped columella, represented by
C. leucomelaenum and
C. stylothecium. ==Description==