[2][3][4] Zeuxine exilis was first formally described in 1906 by Dr Henry Ridley and the description was published in the Journal of the Straits Branch of the Royal Asiatic Society.

Charles William Andrews, a British palaeontologist spent ten months on the island in 1897 and 1898 and although he collected several orchids, did not find Z. exilis.

In October 1904, Henry Ridley, the first director of the Singapore Botanic Gardens made his second, longer visit and crossed the island, including the upper plateau where he collected the orchid he later named Z. exilis, on the 18th of that month.

"[2][4] The species was then not officially recorded for over a century and in the third Christmas Island National Park Management Plan (2002) it was considered "possibly extinct".

[2][6] Then in 2009 it was found and collected by visiting research scientist Peter Green and the discovery was confirmed by Mark Clements.