Clisa australis is a rare, distinctive-looking Australian fly. It lives with bats, likes pit toilets and had been missing for 30 years.

Clisa australis is a species in the family Cypselosomatidae, which are related to stilt-legged flies. This species was described in 1966 by David McAlpine. It was living with bent-wing bats in Carrai caves, near Kempsey, New South Wales (NSW). The caves are home to several animals found nowhere else. 

Rare Australian fly

Clisa australis is the only fly of its kind on the Australian continent. Its closest relatives live in southeast Asia and Lord Howe Island. 

Over [or during] the next couple of decades, scientists spotted the species around northern New South Wales (NSW), and as far south as the Blue Mountains, in habitats including mine shafts and pit toilets. Both bats and flies can swap home in a dark, humid cave for home in a pit toilet.

But in the last several decades, Clisa australis sightings vanished. This left scientists wondering whether the species had disappeared. 

A photograph showing the side profile of the rare Australian fly Clisa australis.
The rare Australian fly Clisa australis.

Hunting for Clisa australis 

Keith Bayless is a research scientist at the Australian National Insect Collection. Keith tracks down new and rare flies for genomics and biodiversity discovery. Since 2015, he’s been on the trail of Clisa australis. 

“As chemical sanitation replaced open pits, this species disappeared from toilets. The main fly species present in chemically treated toilets is a Sylvicola wood gnat, whose larvae are pretty tough and also found in other buildings,” Keith said. 

“But remote national parks sometimes have disused pit toilets. I’ve checked the walls and ceilings of an embarrassing number of public toilets in national parks looking for Clisa australis, without success,” he said. 

Keith also visited Carrai caves, the site where the species was first described. Steep cliffs and stinging plants prevented him entering the caves. Then came Black Summer. 

“A megafire impacted the reserve in November 2019. We don’t know how well the insects and other invertebrates that live in the caves are recovering or whether Clisa australis is still present,” Keith said. 

A photograph showing a white set within the forest floor, used for capturing flies.
A Malaise trap set up to collect flying insects at Barren Grounds, New South Wales. 

A chance discovery of flies 

Last summer, Keith visited Barren Grounds near Jamberoo, NSW, to study flies. His target species was Notoconopinae, a group of parasitic thick-headed flies known from two specimens, which didn’t turn up. Instead, Keith’s luck turned in an unexpected way. 

“Suddenly, in a malaise trap sample from a stream in a dark, humid gully choked with splitting tangle ferns and tree ferns, I finally found a specimen of Clisa australis,” Keith said.

“There are no known caves nearby. The location is hundreds of kilometres from the previous southernmost record of the fly, which was a pit toilet in the Blue Mountains.  

“I found a second specimen, a male, a week later 150km away in an overgrown, muddy ditch at Lake George near Canberra. The fly has never been seen outside of a cave-like habitat before or since. 

“I don’t know whether Clisa australis was always widespread but rare, or whether its range and life history are changing due to human-mediated pressures including megafires, habitat destruction and sanitation,” he said.   

Keith is currently sequencing the genome of Clisa australis to build a family tree of its relationships to other species and learn more about its role in the environment.  

He said finding the species in a fern-filled gully, far from its known habitats, is a good sign.

“This bodes well for both this species and the ability to study it,” Keith said.  

“I’m encouraged that paddling about in bat guano or worse is not a prerequisite for discovering more about this unique Australian fly.” 


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