Pyrenula cryptothelia is characterized by, partly fusedascomata, typically occurring in groups of three or four. It has large sporesmeasuring 32–37 by 13–15.5 μm with three eusepta; a later review of the genus gives a broader sporelengthrange, 30–45 μm. The species is morphologically similar to Pyrenula cubana, but can be distinguished by its larger spores, as P. cubana has spores measuring 21–25 by 8–10 μm.