Jeremy Brent Cramer, 38, of Lacey was charged Tuesday with deliberate homicide and ordered held on $250,000 during his first court appearance in Montana.
Cramer, who reportedly is the boy's father, was arrested Monday night after a clerk reported a man in a convenience store restroom trying to wash blood off his body and clothes.
A statement by the Montana Department of Justice says the man was involved a custodial dispute and took his 3-year-old son from Lacey.
A family friend told KOMO News Cramer asked his wife Natalie if she wanted to go for a drive Monday morning, and she declined. So he took the child.
"He took his son all the time with him on trips and kept him with him a lot," said neighbor Ed West.
But the mom called police in Lacey after her husband wasn't answering cell phone calls or text messages. She also said that his fuel card was used in Moses Lake earlier in the day.
However, the mother told police she did not believe the boy was in any danger, so no Amber Alert was issued, said Lacey Police Cmdr. Jim Mack.
"He was with his custodial father, they lived together at the home," Mack said. "The mother did not alert us that she believed the father would harm the child, or that the child was in any danger, because they all live together at the home."
Instead, police issued a law enforcement alert requesting law enforcement agencies in Washington, Idaho and Montana to be on the lookout for the father's vehicle.
Police in Montana took Cramer into custody late Monday after being contacted by the convenience store clerk. His son was not with him.
Cramer's vehicle was found 5 miles southeast of Anaconda around sunrise on Tuesday morning. The boy's body was found a short distance away. His name was not released.
The boy's mother was notified shortly after his body was found.
"When investigators went to the home this morning she was in disbelief that he could have done this," Mack said.
Mack said that the couple had been arguing about finances recently.
"He had asked her earlier within the last couple of weeks if they could do a road trip to the East Coast, and she said, 'No, we don't have the money,'" Mack said. "It sounded like he wanted to go to the East Coast."
Agents with the state Division of Criminal Investigation are assisting Anaconda-Deer Lodge Law Enforcement in the investigation.
"You don't know who to feel sorriest for," said family friend Ed West. "(The boy) laying in the field, the dad in jail or Natalie here suffering for all of it. It's just a devastating thing."