Gyrotrema papillatum has a grey-green to olive-green thallus adorned with numerous white papillae. The cortex is prosoplectenchymatous–made of a dense, tightly interwoven layer of fungal hyphae. The photobiont layer and the medulla beneath often contain clusters of calcium oxalate crystals. The apothecia of G. papillatum are prominent, with a rounded to lobate shape, measuring 1–1.5 mm in diameter. The exposed disc of the apothecia is a cinnabar-red colour. Around this disc, the margin is lobulate to recurved and fused, sharing the same cinnabar-red hue on the inside. This species lacks a columella, but instead has concentric rings of excipular tissue that separate rings of old hymenia. The youngest hymenium ring is situated closest to the margin. The excipulum is prosoplectenchymatous and carbonised, and lacks periphysoids. The hymenium stands 80–100 μm high, and the paraphyses are unbranched.[1]
Each ascus contains eight ascospores that have between 5 and 9 septa (internal partitions), measuring 25–30 by 6–8 μm. These ellipsoid spores have thick septa and lens-shaped lumina, are colourless, and has a violet-blue reaction when treated with iodine (amyloid reaction). The apothecial disc contains an unidentified type of anthraquinone substance.[1]