A Southland police SAR team today recovered the bodies from an area below Marian Peak.
The pair were reported missing yesterday afternoon and had been overdue for 24 hours, police said this evening.
A search by helicopter yesterday evening found the climbers at the base of a climbing face, where they had clearly fallen, Sergeant Tod Hollebon, of Te Anau, said.
The pair left Homer Huts near the Milford Road on Saturday and their intended route was Barrier Knob to Barrier Peak, a descent into Marian Valley and to ascend Marian Peak.
Police are contacting next of kin.
Southern Lakes Helicopters owner Richard Hayes flew the chopper that searched for the climbers last night.
He was called to find the pair after they were reported overdue by a third climber. Hayes first flew to Homer Huts to pick up the man who raised the alarm.
The bodies were found around 6pm as the sun was setting. Police were on board but the terrain was so tricky it was decided to wait till daylight to recover the bodies.
The pair were members of the New Zealand Alpine Team, on what has been described as one of New Zealand's most difficult climbs.
The alpine team's website says it is made up of New Zealand alpine climbers who volunteered their time to mentor a future generation of alpine climbers.
It takes applicants aged between 18 and 25 and provides three years of training to further their climbing skills.
A New Zealand Alpine Team member said the area the two men were climbing was one of New Zealand's bigger mountain faces.
