It is a rare plant, only known from three small populations and currently meets the requirements of the World Conservation Union (IUCN 2000) Red List Category "Endangered".

[2][3][4] Verticordia hughanii was first formally described by Ferdinand von Mueller in 1878 and the description was published in Fragmenta phytographiae Australiae from specimens collected by Allan Hughan.

[1][5] The specific epithet (hughanii) honours Hughan, a grazier and plant collector from Swan Hill[6] who collected the type of this species and four other verticordias.

[2] When Alex George reviewed the genus in 1991, he placed this species in subgenus Eperephes, section Verticordella along with V. pennigera, V. halophila, V. blepharophylla, V. lindleyi, V. carinata, V. attenuata, V. drummondii, V. wonganensis, V. paludosa, V. luteola, V. bifimbriata, V. tumida, V. mitodes, V. centipeda, V. auriculata, V. pholidophylla and V.

[8][9] Verticordia hughanii is classified as "Threatened" by the Western Australian Government Department of Parks and Wildlife[8] meaning that it is likely to become extinct or is rare, or otherwise in need of special protection.