The small duck orchid was first formally described in 1840 by John Lindley from an incomplete description by James Drummond in Edwards's Botanical Register. Drummond had given it the name Caleana nigrita and Lindley published his description in A Sketch of the Vegetation of the Swan River Colony. In 1972 Donald Blaxell changed the name to Paracaleana nigrita but the name change has not been accepted by the World Checklist of Selected Plant Families and in 1989 Mark Clements noted that none of the characters used to separate Paracaleana from Caleana is "sufficiently significant" to maintain two genera. The specific epithet (nigrita) is a Latin word meaning "blackened".
