The species was first described as new to science by American mycologist William Alphonso Murrill in 1912, based on collections he made in November, 1911 under Californian redwoods.
Agaricus hondensis has traditionally been classified in the section Xanthodermatei, a grouping of Agaricus species related to A. xanthodermus that are characterized by fruit bodies with phenolic odors, temporary yellowing discolorations in some parts of the fruit body, a negative Schaeffer's reaction, and toxicity.