Police have named 77-year-old Whetuki Sam Kopua and 60-year-old Matekino Lucy Burling, both of Owaka, as the people missing in the Catlin area.
A 60-strong search team made up of police, the NZ Rescue Co-ordination Centre, marine SAR and volunteers have been hunting today for the Mr Kopua and Ms Burling, who were meant to return to shore last night.
The boat has been located, but they were not aboard.
Police said a boat had been found today just south of Nugget Point where the teams were searching but did not confirm if it was the missing boat.
"Divers have been in the water searching the area around the board, but nothing has been located," police said in a statement.
Teams will now focus their search on a wider area.
The alarm was raised about 6pm yesterday when an overdue boat in the Catlins area did not return.
Last night a marine search and rescue operation was launched, running out of Owaka and involving rescuers from south Otago and Dunedin.
Fog hampered the search efforts overnight but a large-scale search was launched again this morning.
The missing pair are both from Owaka and were on a fishing trip in their silver 5.2 metre pontoon-style Kiwicraft boat, called Krystella.
Police say they left Catlins Heads about 8.30am yesterday and were expected back before dark.
Searchers are continuing to look in areas north and south of where Mr Kopua's boat was found overturned.
There have been coastal searches of beaches, aerial searches with helicopters and an aeroplane, plus boats have been on the water all day looking for the missing persons.
The search will continue through the day and again tomorrow.