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The fires have been particularly bad on Kangaroo Island, which is known as the Australian equivalent of the Galapagos Islands as a result of its diversity.
There are fears that populations of small marsupials called dunnarts and glossy black cockatoos might have been completely eradicated by the fires that have consumed around a third of the island.
What has been left has been described as a 'scorched' wasteland.
After the danger has passed, conservationists hope to discover any surviving animals from the dunnarts population in order to save them 'before they are completely gone'.
Heidi Groffen, who works as an ecologist and co-ordinator for the non-profit organisation Kangaroo Island Land for Wildlife, said the tiny dunnarts, which are about the size of a mouse, can't outrun the fires because they are too small.
She fears that the 300-strong contingent on the island could have been completely destroyed.
However, she retains hope that some might have found shelter in rocks and other small safe spaces.
She said: "Even if there are survivors, there is no food for them now.
"We're hoping to bring some into captivity before they are completely gone."
Pat Hodgens, a fauna expert for the Kangaroo Island non-profit, also told The Independent: "It's early days, fires are still burning but we have lost a lot of critical refugia [areas where animals can survive during harsh conditions] for endangered species which will affect long term viability of these species.
"The Kangaroo Island dunnart is our main species of concern and it looks like its entire known [habitat] range has been fried. We are locating unburnt remnant patches of its habitat to see if we can locate it through camera trapping."
Now that the fires have mostly passed, Hodgens said that the group has set up camera traps to help spot any survivors, and are using drone mapping in the hopes of discovering any places that the marsupials could still be surviving.
As well as the dunnart, more than half the 50,000-strong koala population of the island is also feared dead, and a rare flock of black cockatoo's future on the island is in doubt as their habitat has burned down.
On top of the death toll, many animals have also been injured in the fires.
Sam Mitchell, co-owner of the Kangaroo Island Wildlife Park, said: "We are seeing kangaroos and koalas with their hands burned off - they stand no chance. It's been quite emotional.
"We will do whatever we can to rehabilitate the native wildlife but it's going to take years to recover."
These circumstances are not limited to Kangaroo Island.
The University of Sydney's Professor Chris Dickman told 7 News: "There are a lot of people out there helping by going into areas that have been burned to look for koalas and any other native wildlife [that have] been affected.
"In the longer term, the rebuilding of populations of many native species is going to be the issue.
"A lot will have been undoubtedly very badly affected by these fires."
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