South Dakota Game, Fish and Parks have seen an outbreak of Epizootic Hemorrhagic Disease, or EHD, this year.
The disease is spread through deer after they are bitten by midges (small flies) during wet spring and dry fall months.
More than 2,000 deer have been reported dead due to the disease in 2016.
In 2012, EHD killed more than 3,700 deer.
Game, Fish and Parks Regional Terrestrial Resource Supervisor Josh Delger said it’s the biggest outbreak in the state since 2012.
He also said the return of the disease comes at a bad time.
"We're just actually getting at the point now where we're about recovered from the last outbreak in some of those areas and now they're getting hit again so it's actually been detrimental in that respect,” said Delger.
He said EHD hasn't affected the entire state with few reports coming from the southeast part of the state.
"It's been most prevalent in the Huron areas, down towards Chamberlain and up towards Pierre is where we've seen a lot of our mortality,” said Delger.
For hunters in the state, Delger said Games, Fish and Parks took steps to help with the down population.
They offered refunds for licenses while also removing heavily affected areas from license drawings.
As for future years, Delger said getting deer numbers back up isn't going to be a quick fix.
"It'll be several years before we see them make a real good comeback from it,” said Delger.
With colder temperatures coming across the state, Game, Fish and Parks expects midge numbers to go down.
There is no way of helping deer fight EHD other than hoping for unsuitable weather for the disease.
Delger said deer do not live long once they contract EHD.
The disease is not transmissible to humans but they advise not eating meat from a dear that appears sick, such as skinnier than usual appearance, minimal movement or swelling on the deer's mouth or face.