Police in New Mexico's capital Santa Fe confirmed the remains as those of Randy Bilyeu from Colorado.
He went missing in January this year hunting for a $2m (Â£1.5m) trove hidden by art dealer and author Forrest Fenn.
Thousands have searched for the hoard left by Mr Fenn, who gave clues about the treasure's location in a 2011 book.
Bilyeu set out for the Rocky Mountains in northern New Mexico with a raft and his pet dog on 5 January.
His wife reported him missing on 14 January, and the raft and dog were found the next day. The remains were discovered along a stretch of the Rio Grande river.
Mr Fenn has urged people not to search for the treasure during winter and joined in search efforts to find Bilyeu.
The writer says hunters should not look in "any place where an 80-year-old man couldn't put it".
A Texan woman got lost searching for the treasure three years ago but was found by rescuers.
The remains of a 54-year-old man who disappeared hunting for a hidden stash of gold and jewels in New Mexico have been discovered, local authorities say.