This species is characterized by its thin-textured lanceolate leaves with quite short petioles, slender rather short flexuous inflorescences, calyx lobes that are markedly unequal in size, short white corollas, and small white fruits. The four calyx lobes are generally 0.8-2 mm long with one of them slightly larger to twice as long as the others. The corolla tubes are ca. 3 mm long.

Gonzalagunia rudis similar to and had been confused with Gonzalagunia ovatifolia. These were separated by Taylor (in Lorence et al. 2012) by their calyx lobes, obtuse to rounded and glabrescent in Gonzalagunia ovatifolia vs. acute and densely pubescent in Gonzalagunia rudis, and wider larger leaf blades (4.6-17 x 2-8 cm) in Gonzalagunia ovatifolia vs. narrower smaller leaves (3-11 x 1.5-5 cm) in Gonzalagunia rudis. Gonzalagunia rudis is also similar to Gonzalagunia osaensis of southern Costa Rica and western Panama, which has 2-locular ovaries and fruits (vs. 4-locular in Gonzalagunia rudis).