Anthony Michael Sanders was charged with capital murder in the December death of Ellie Sanders at the family's suburban home in the US state of Texas, Watauga police said.
He is accused of suffocating his daughter while caring for her and his five-year-old son.
Investigators believe an enraged Sanders bruised Ellie all over her body, bit her on her back and murdered her by holding her down with his hand over her face, police officials said.
Tarrant County medical examiners ruled earlier this month that the infant's death was a homicide by asphyxiation.
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Sanders was asked to take care of Ellie and his son while his wife went to an art show, according to an arrest affidavit cited by the newspaper.
The boy discovered his sister in a bedroom and "tried to wake her up and she would not wake up", Babcock said.
Sanders could not explain her injuries and claimed he had changed Ellie's diaper about a half hour before his wife came home, according to investigators.