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 about 2am on Tuesday, and winched two members of the party - a 44-year-old man and a 13-year-old boy - to safety from a reef.

Placid seas raised hopes that the other three occupants of the boat were still alive, but they were dashed after rescuers recovered two bodies later in the morning.

The fifth and final member of the crew was found dead shortly after 2pm.

The rescued pair were taken to Port Lincoln Hospital with non-life threatening injuries.

They were treated for conditions related to hypothermia as a result of exposure to the cold, Superintendent Paul Bahr told reporters on Tuesday.

"The boat itself has also been located and is on its way back to Port Lincoln," Supt Bahr said.

"That will be offloaded later today and will be subject to further forensic examination and any examination the coroner may require."

The fishing party comprised family members and close friends, and aside from the one rescued teen were all adults.

The two rescued anglers told police their boat was swamped by a wave about 4pm on Monday, overturning the vessel and throwing all aboard into the water.

A large-scale rescue operation was launched after family members of the crew alerted police about their non-return just after 8.30pm on Monday night.

As well as the police helicopter, police water operations, local Sea Rescue vessels, a Challenger jet plane and P&O cruise ship the Pacific Explorer took part in the search.

Police will now prepare reports for the coroner.

Australian Associated Press