The FBI lab in Quantico, Va., made the identification, Sheriff Rocky Watson said. No other details were provided in a terse press release.
The identification ends any hope that the child might have been found alive, as his 8-year-old sister Shasta was a week ago.
The two children were missing from the home where their mother, brother and mother's boyfriend were bound and bludgeoned to death. The bodies were found May 16 in their rural home near Coeur d'Alene, Idaho.
Authorities believe they were abducted by registered sex offender Joseph Edward Duncan III and spent part of the time at the remote camp site in the Lolo National Forest where the remains were found.
Shasta was rescued early July 2 after employees and customers spotted her with Duncan at a Coeur d'Alene, Idaho, restaurant a few miles from her mother's home and called police.
Information she provided, along with other evidence, led authorities to the campsite.
So far, Duncan has only been charged with kidnapping Shasta and Dylan.
But authorities have said they believe he also killed their mother, Brenda Kay Groene, 40; their brother, Slade Groene, 13; and the mother's boyfriend, Mark Edward McKenzie, 37.
Watson said Friday that the family appeared to have been chosen at random but that the attack was carefully planned and executed, possibly with the motive of abducting the young children for sex.