The bodies of Sean Wilkinson and Clay McKemie of Rome, Ga., were found with their overturned kayak about 5½ miles west of the Suwannee River, the Coast Guard said in a statement.
They had become lost Saturday while kayaking with a school group in an area about 100 miles north of Tampa. They were believed to have been wearing life vests.
The boys had not been seen since they set out with eight other people who traveled to Dixie County from Darlington High School in Rome for a kayaking and camping trip.
The other eight were found Sunday about seven miles from the mouth of Suwannee River, said Florida Fish and Wildlife Conservation Commission spokeswoman Karen Parker.
The group had headed north in the Gulf of Mexico and intended to skirt the coastline for 4½ miles until arriving at Coon Island, where they planned to spend Saturday night, said FWCC Capt. John Burton. The group, which included several kayaks and canoes, was led by a motorized catamaran raft.
During the trip, the choppiness of the water and the inexperience of the kayakers led some boats to get separated from the group, Burton said.
As the catamaran neared Coon Island, a chaperone on board began circling back to try to round up some of the lagging boats. But the boat's motor quit as it began to get dark.
All but one of the kayaks tied up to the raft, as 2 to 3 foot waves developed in the gulf amid scattered rains and high winds, Burton said.
About 9 p.m. Saturday, one of the chaperones, with a teenager, began searching for the missing kayak because they thought they saw a light in the distance.
But they became lost as well, and the two paddled for three to four hours until the chaperone was finally able to use his cell phone. He called his wife in Georgia, who then called the Coast Guard.
A Coast Guard helicopter located the six kayakers tied up to the raft at about 3 a.m. Sunday and a rescue boat brought them to shore. About an hour later, the helicopter located and hoisted the kayak with the chaperone and teenager aboard.
The kayaking tour was led by an English teacher at the private Darlington School, Steve Hall, who is a licensed outdoor tour guide and leads several weekend adventure trips for teens throughout the year. A spokeswoman for the school said Hall, who has 25 years in outdoor education experience, has led a similar trip to that area for seven years and never had any safety problems. According to Hall's outdoor education trip Web site, he is an experienced river rafting guide.
The students were on spring break from the school, a Darlington spokeswoman said.