The genus is characterized by its unique structure, featuring densely arranged filaments composed of cyanobacteria (blue-green algae) wrapped in fungal threads.

The genus was circumscribed in 1917 by American scientist Lincoln Ware Riddle, based on specimens collected in Florida.

[6] This material was originally found growing on the bark of scrub oaks at West Palm Beach, Florida.

This unique combination of morphological and anatomical features distinguishes Pyrenothrix from other lichen genera and contributes to its classification within the Pyrenotrichaceae.

[5] The photobiont of Pyrenothrix nigra has a filamentous cyanobacterial structure with double-false branching, a characteristic traditionally associated with the genus Scytonema.

This proposition is considered plausible due to ongoing debates about the reliability of branching patterns as a distinguishing feature between Scytonema and Rhizonema.

[9] Rhizonema, a recently resurrected cyanobacterial genus, was established to classify filamentous, heterocyte-producing photobionts previously thought to be Scytonema, but genetically distinct based on 16S rRNA sequences.

[9] The exact nature of the photobiont in Pyrenothrix remains uncertain, highlighting the need for more extensive genetic sequencing to clarify the taxonomic boundaries and symbiotic relationships within lichen associations.

[9] The cyanobacterial photobionts in Pyrenothrix, whether Scytonema or Rhizonema, are known to produce heterocytes, specialized cells capable of nitrogen fixation.

This ability to fix atmospheric nitrogen into biologically usable forms is ecologically significant, potentially contributing to nutrient cycling in the environments where these lichens occur.