Officials said Ethan's body was identified through DNA analysis extracted through bone marrow.
Ethan is seen on the floor in this family photo. The suspect in his death and disappearance of his sister, James DiMaggio, is seen on the far right.
Ethan's 16-year-old sister Hannah Anderson remains missing, and the search for her and her suspected kidnapper is focused on Idaho.
Earlier on Friday, officials said the two were spotted by horseback riders in the Idaho wilderness. His car, a blue Nissan Versa, was found hidden in brush.
The horseback rider's impression of the pair was "it seemed odd but nothing as alarming," a spokeswoman for the Ada County Sheriff's Office said.
"They did speak and exchange pleasantries. I don't think there was a lot of information exchanged," she said. "He left the conversation believing they were camping in the area."