Cook County prosecutors say Lakesha Baker and her boyfriend, Michael Scott, both of Maywood, entered their pleas Thursday during an arraignment.
The 22-year-old Baker and 21-year-old Scott are accused of killing Bryeon Hunter on April 15 and dumping his body in the Des Plaines River.
A body matching the boy was recovered from the river last week. DNA samples have been taken from Baker and the boy's grandmother to determine the identity of the body. Authorities say the cause and manner of the child's death hasn't been determined.
Baker, who initially claimed her son was kidnapped, is being held without bond. Scott is being held in lieu of $750,000 bond.