Arachnothryx brenesii is characterized by its tree habit, petiolate leaves with strigose-sericeous pubescence on the undersides, long spiciform or racemiform inflorescences, white somewhat small corollas, and small subglobose capsules. This species grows to a relatively large size for Arachnothryx and related genera. The distinctive silky leaf pubescence is often deciduous. The inflorescences have a well developed primary axis with the flowers borne in subsessile condensed cymose along it: the arrangement is thyrsiform, but the general appearance is spiciform.

In general aspect Arachnothrux brenesii is similar to Gonzalagunia, and without fruits it cannot be separated from that genus. Arachnothryx brenesii was in fact described at one time as Gonzalagunia exaltata, based on a flowering collection. Arachnothryx brenesii has also been confused frequently with Gonzalagunia brenesii, a distinct species. This confusion is due in part to another Gonzalagunia species that also grows in Costa Rica having the the same species epithet, "brenesii", along with a general morphological similarity. Gonzalagunia brenesii can be separated by its fleshy fruits, smaller shrubby habit, and subsessile leaves without strigose-sericeous pubescence.