This species was first formally described in 2003 by Marco F. Duretto who gave it the name Boronia montimulliganensis in the journal Muelleria. The specific epithet (montimulliganensis) refers to the isolated Mount Mulligan, the only place where this species is known to occur. In a 2013 paper in the journal Taxon, Marco Duretto and others changed the name to Cyanothamnus montimulliganensis on the basis of cladistic analysis.
