The species was first reported by French mycologist Roger Heim in 1956 as a variety of Psilocybe mexicana before he officially described it under its current name a year later.
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bonneti is named after Dr. Federico Bonet (died 1980), emeritus professor of the Escuela Nacional de Ciencias Biológicas, who assisted Guzmán with his doctoral studies.
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The species was first mentioned by French mycologist Roger Heim in 1956 based on material collected by American ethnomycologist R. Gordon Wasson in Paso de Cortés, on the slopes of Popocatépetl mountain in Mexico.