The Orange County Medical Examiner said thatEMS crewsarrived at the family's Mebane home at 5:38 a.m. Thursday.
Emergency workers say the parents told them that 2-year-old Glasya Lynn Cook was not responsive.
The emergency crews alerted the authorities, who sent the baby's body to the State Medical Examiner's Office.
The Examiner's Office called the incident a case of Shaken Baby Death Syndrome. The Orange County Sheriff's Department calls it a case of second degree murder.
James Russell Smith Jr., 36, was charged around 4:45 p.m. Thursday.
Investigators say the stepfather has an explanation.
"The father did say that he spanked her last night and popped her in the mouth," says Sgt. Ned Thorpe with the Orange County Sheriff's Department. "As for how strong and how many times she was spanked, he said two or three small licks on the buttocks, that's his statement."
The Sheriff's Department says the suspect has previously been charged with child abuse.
The girl's mother, 20-year-old Angie Smith, has not been charged, although authorities say she was home at the time of the incident.
Smith is now staying somewhere else. Relatives who returned to the house to pick up some of her belongings say the family is holding up remarkably well.
"The family is doing real good right now," says William Boggs, the toddler's uncle. "Everybody has pulled together and are supporting each other. We are just trying to do the best we can."