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The mother and her boyfriend are being held on $1 million bail in Santa Ana.
Police say 27-year-old Alberto Guzman and 25-year-old Gabriela Morales were taken into custody after Morales' 4-year-old son died under suspicious circumstances.
Police were called to the couple's apartment in Santa Ana Friday afternoon. Medics found the boy in full cardiac arrest. He was transported to the hospital where he was pronounced dead.
"When medics arrived they immediately felt that the child's condition was suspicious. The child had visible signs of trauma on his head and he had numerous bruises throughout his body," said Cpl. Jose Gonzalez from the Santa Ana Police Department.
An autopsy found the cause of death was trauma to the boy's head. Police say the alleged abuse had been happening for about two months.
Police say the couple told them that they were disciplining the child.
The boy had been living with his 7-year-old sister and 9-year-old brother in the apartment. The three had moved to Santa Ana from Mexico seven months ago.
There were no signs of abuse involving the older children. The brother and the sister are now in protective custody.
The mother and her boyfriend remain in jail and are facing murder charges.