Runte was one of two men on a 34-foot sailboat that capsized in rough waters at about 4:25 p.m. Friday just south of Pillar Point, Coast Guard spokesman Lt. j.g. Jeremy Pichette said.
After the boat turned over, the Coast Guard received a report that a flare was spotted in the area, Pichette said. Two boats and a helicopter were launched as part of a joint rescue effort.
Pillar Point Harbor patrol, the San Mateo County Sheriff's Office, the Half Moon Bay Fire Department and state parks officials assisted in a shoreline search.
Harbor patrol officers rescued Runte's shipmate shortly after the flare was spotted, Pichette said.
A Coast Guard helicopter spotted Runte at 5:37 p.m. Harbor patrol pulled him from the water and immediately administered CPR, Pichette said.
Runte was taken to Seton Coastside Hospital in Moss Beach and was pronounced dead by local paramedics, Pichette said.
Pichette said Runte and the other passenger were not wearing life jackets or full-body immersion suits.
The National Weather Service issued a high surf advisory on Thursday that will remain in effect throughout this afternoon, so the Coast Guard is advising mariners to avoid the water if they can.
"Even the most experienced mariner can be faced with a situation that they may not be ready to handle," Pichette said.
Beachgoers are also being urged to keep a safe distance from the waterline.
Friday's incident off Half Moon Bay was this Thanksgiving weekend's second fatal boat accident in the Bay Area. On Thursday, an elderly couple died after their boat capsized in the waters off Bodega Bay. The Sonoma County coroner's office said their identities were being withheld pending notification of their families.