The two victims were part of a family visiting from Southern California was hiking near the Vernal Fall Footbridge. Group members were cooling off in the river Wednesday when a current carried the boys away.
The older boy was pronounced dead around 3 p.m. Wednesday. Park visitors were able to pull him from the river about 150 yards downstream, but efforts to resuscitate him failed.
Authorities were still searching for the younger boy, who is presumed dead. Their mother was hospitalized after being pulled from the river with a back injury, park spokeswoman Kari Cobb said.
"She went into the river but made it out," Cobb said.
The names of the boys were not immediately released.
The bridge is a vantage point on the Mist Trail where Vernal Fall first comes into view. The location was the site of tragedy last summer when three Central California friends cooling off in a pool above the fall were swept to their deaths.
Two of their bodies were found months later lodged under boulders near the site where the 10-year-old was found.
The Merced River runs through the heart of Yosemite Valley, and the Mist Trail to the fall is one of the most popular and sometimes perilous hikes in the park. The river falls 317 feet straight down to a narrow gorge filled with boulders the size of cars then descends another 400 feet by the time it reaches the bridge. Even when the rest of the river is moving slowly, the drop in elevation and narrow channel cause the water to move swiftly.
The boys were part of group of about 15 extended family members who made the short hike to the bridge, park spokesman Scott Gediman said. While signs at the trailhead warn that the river can be dangerous, people often are drawn to the water's edge.
"We've got a low water year this year, and around the banks it's only 8 to 10 inches deep, but once you get our further we have a swift current and it gets deeper," Gediman said. "They both got swept away by the current."
The Mist Trail remained open during search and rescue operations but portions might be closed depending upon developments.
A 57-year-old man drowned two weeks ago in the Merced River when he was pinned under a rock, and another person died in June on the South Fork of the river near the Wawona area on the south end of the park.
The Associated Press contributed to this report.