Zapatadon was first described and named by Víctor-Hugo Reynoso and James M. Clark in 1998, and the name of the genus is a homage to the Mexican revolutionary leader Emiliano Zapata, added to the Greek sufix -odon, "tooth", common in other sphenodontian taxa; the name of the type species, ejidoensis is in gratitude to the people of the ejido (communal land area) of El Huizachal, that allow the investigation of the fossils.