This species is characterized by its shrubby habit, appressed strigose pubescence, somewhat stiff-textured leaves that are subsessile to shortly petiolate and rounded to truncate or cordulate at the base, flowers borne on short secondary axes along the primary axis, white to pink corollas with tubes 6-12 mm long and lobes 3-5 mm long, white fruits with four ovary locules, and lowland habitat. This species is a relatively narrow endemic; some other Rubiaceae are also endemic in this same region.
Gonzalagunia brenesii is similar to Gonzalagunia rosea, which has thin-textured leaves that are rounded to acute at the base, generally longer petioles, and pink corollas. Gonzalagunia brenesii is also similar to Gonzalagunia longithyrsa, which is found in premontane vegetation and has shorter corolla lobes, ca. 2 mm long.
Gonzalagunia brenesii has also been confused with Arachnothryx brenesii, which is a separate species that also has a spiciform inflorescence and grows in Costa Rica. This confusion is due in part to the treatment of Arachnothrux brenesii but some authors as i>Gonzalagunia exaltata, and these species having the same species epithet, "brenesii". Arachnothryx brenesii can be separated by its capsulare fruits, larger tree habit, and petiolate leaves with desne strigose-sericeous pubescence on the undersides.