Police in Port Huron, Mich., issued arrest warrants for John William Gonzales, 38, and Ashley Marie Snowden, 23, the parents of Braylon Bishop Gonzales.
Police believe Braylon died in Port Huron in 2005 but have not explained why they think that is the case.
Gonzales is being charged with murder, child abuse and being a habitual offender, while Snowden is facing a charge of being an accessory after the fact to a felony.
Police found a child's body wrapped in a plastic bag and placed in a storage container in the Fort Wayne home that Gonzales and Snowden shared. Fort Wayne police have said they believe the body had been encased in concrete at some point.
Officials identified the body as Braylon but are checking DNA to confirm that.
Police made the gruesome discovery after getting a tip there might be a body inside Gonzales' Raymond Avenue home, reports CBS News affiliate WANE-TV.
An autopsy Thursday revealed that the child died of blunt-force trauma to the head, the Allen County Coroner's Office said. The death is being investigated as a homicide, although it hasn't been ruled as such yet.
Three children living in the home with Gonzales and Snowden, ages 5, 2 and 6 months, have been taken by Child Protective Services, Fort Wayne police said.
Gonzales' sister, Marlo Harley of Fort Wayne, said her family had not seen Braylon in years. Gonzales would make occasional appearances at family members' homes, but always alone, she said.
"We asked about the kids, and he said they were fine, and we asked him to bring them over, and he always had some excuse," Harley said.
Police in Port Huron are taking over the investigation and evidence has been turned over to them, said Allen County Coroner Jon Brandenberger.