Pyrenula borneensis is characterized by a thin, continuous and smooth
thallus with a , and with a distinctive pinkish-white colouration. It lacks
pseudocyphellae or crystal-containing pockets. The lichen forms a symbiotic relationship with algae (i.e., from the
green algal genus
Trentepohlia. Its ascomata (fruiting bodies) are in form, , and dispersed across the surface of the thallus. They are conical and slightly emerge from the surface, measuring about 0.5 to 1.3 mm in diameter. These structures are black and distinctly lack a covering layer of the thallus around their edges. The ascomatal wall is only on the upper part, extending horizontally to form a shield-like about 150
μm thick; it does not react to
staining with
potassium hydroxide (KOH–). The
ostioles, located at the apex of the ascomata, are black and similarly do not react to KOH. Internally, the (the sterile tissue inside the fruiting body) is transparent and densely filled with oil droplets. The
asci are cylindrical to club-shaped (cylindrico-), each containing eight
ascospores arranged in a single row; they do not have an
iodine staining reaction (IKI–). are brown, , and in shape, typically featuring three primary transverse
septa and two to five internal compartments () per row. These spores measure roughly 20–26 μm in length and 10–12 μm in width, with rounded ends and lumina that vary from rounded to irregularly elongated. There is no constriction at the septa. No
pycnidia have been observed in this species, and chemical analysis has not revealed the presence of any detectable
secondary metabolites (
lichen products). ==See also==