Holyhead Coastguard received a 999 call on Sunday reporting the pair, believed to be from Birmingham, had got into difficulty off Barmouth beach.
The RNLI said the sea search was suspended at 18:30 BST, though a search of the shoreline is continuing.
A Coastguard spokeswoman said there had been an "intensive search" for the boys, reportedly aged 14 and 15, but "sadly they have not been found".
"It looks like there were two people in difficulty and another person in their same group went in to help," she said.
"That person managed to get out of the water - both the other two were still in difficulty."
She said the Coastguard had been told one person had been seen to "disappear under the water".
Rescue teams from Barmouth, Aberdovey and Fairbourne and a helicopter from Caernarfon joined the search.
The RNLI said: "Barmouth RNLI's inshore lifeboat was requested to launch by HM Coastguard at 13:40 and the station's all-weather lifeboat was launched 10 minutes later."
It said other teams joined the search, but it added: "Shortly before 18:30 HM Coastguard suspended the sea search and the RNLI lifeboats returned to their respective stations.
"They will be made ready to relaunch as and when requested by HM Coastguard."
The Welsh Ambulance Service and North Wales Police also attended.
Two teenagers have been reported missing off the coast of Gwynedd.