Experts said the "remarkable" species is the only orchid known to consistently flower at night, but why it has adopted this behaviour remains a mystery.
"It was so unexpected because there are so many species of orchids and not one was known to be pollinated at night," Andre Schuiteman, senior researcher and an orchid expert at the Royal Botanic Gardens, Kew, told BBC News.
"It was quite remarkable to find one, after so many years of orchid research, that is night-flowering," he said.
The specimen was discovered by co-author Ed de Vogel during a field trip in a region of lowland rainforest on the Southeast Asian Island.
Although the tiny Bulbophyllum nocturnum is the first known night-flowering orchid, it is not uncommon for plants to flower at night. Most orchids though, flower both day and night.
Though it is not clear exactly what pollinates Bulbophyllum nocturnum, scientists think nocturnal flies carry out the job.
The specimen has been identified as belonging to the Bulbophyllum genus, which - with about 2,000 species - is the largest group in the orchid family.
Schuiteman said the exact reason why B. nocturnum only flowered at night would remain a mystery until further field studies had been completed.
The findings appear in the Botanical Journal of the Linnean Society.