Emergency crews began a frantic water and air search on Monday evening after the boat and its five occupants did not return to Port Lincoln.
A police rescue helicopter located the upturned boat near Spilsby Island in the Spencer Gulf early on Tuesday morning, and winched two members of the party - a man and youth - to safety from a reef.
The rescued pair were taken to Port Lincoln Hospital with non-life threatening injuries but were being treated for conditions related to hypothermia as a result of exposure to the cold, Superintendent Paul Bahr told reporters on Tuesday.
"I can also advise a short time ago we located a deceased person in the water in the same location," Supt Bahr said.
"At this stage we don't know who that person is, they are yet to be identified.
"The boat itself has also been located and is on its way back to Port Lincoln. That will be offloaded later today and will be subject to further forensic examination and any examination the coroner may require."
The fishing party were family members and close friends, and aside from the one rescued youth were all adults.
The two rescued fishers told police their boat was swamped by a wave about 4pm on Monday, overturning the vessel and throwing all aboard into the water.
The search continues for the other missing crew members.
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