Polymeridium endoflavens was formally described by the lichenologists André Aptroot, Danyelly Santos Andrade, and Marcela Eugenia da Silva Cáceres in 2016.

The type specimen was collected in Mata do Junco, Santa Luzia do Itanhy, Sergipe, Brazil, at an elevation of approximately 150 m (490 ft), by the second author.

[2] The thallus of Polymeridium endoflavens is not corticate, dull, continuous, covering areas up to 2 cm (3⁄4 in) in diameter, and whitish in colour.

Ascospores are hyaline (translucent), 5–7-septate, fusiform, measuring 32–37 by 10–13 μm, with pointed ends and rounded lumina, and are not surrounded by a gelatinous layer.

Thin-layer chromatography analysis reveals the presence of lichexanthone, a lichen product that causes the thallus to fluoresce when lit with a long-wavelength UV light.