Desie Horton, 29, and Trevor Bishop, 30, both pleaded not guilty to the charges they face in the case.
Bishop is charged with assault and felony child abuse. If convicted, he faces life in prison.
Visalia police believe Bishop beat the toddler last week at the home, he and Horton shared.
The child's mother is facing felony child abuse charges for failing to protect the boy, who remains in a coma and in critical condition.