Deputies took Earl Kimrey, 32, into custody Friday night, as the search continued for Kristy Woods' daughter.
Authorities said they have not yet located Mariah's body, and the missing persons search that included Federal Bureau of Investigation agents and K-9 units will now shift to a recovery effort.
Kimrey "secretly disposed of the dead child's body", the warrant said.
Onslow County deputies say they charged 32-year-old Earl Kimrey with concealing a death.
In a news release Saturday, the sheriff's office also stated that it believes the toddler is dead. "All with one mission: to help us find Mariah".
Mariah's mother told the Onslow County Sheriff's Office that she last saw her daughter at their family home, at 2404 Dawson Cabin Road in Jacksonville, on Sunday night when she put her to bed.
People with surveillance footage near where a 3-year-old girl disappeared in eastern North Carolina are being urged to call police and share the video as they investigate the girl's death.
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'Someone just walked right up in there, grabbed the 3-year-old out of the bed and she didn't cry, she didn't scream?
The FBI said in a statement on Friday that the search for Mariah Woods took deputies from the New Hanover County Sheriff's Office to a local creek, where they used sonar. The FBI said Thursday that it is testing "items of interest" at its lab in Quantico, Virginia.
The investigation is ongoing.
Authorities say the man charged in the disappearance of a young North Carolina girl is the boyfriend of the child's mother.
Mariah Woods is described as a white female with brown hair and blue eyes, about 2-foot-9 weighing about 30 pounds.
Onslow County Sheriff Hans Miller talked during a news conference about Mariah Woods, who vanished November 27 from her home on High Hill Road. Please just bring her back safe and sound - she's my baby, she's my everything'.
FBI Special Agent-in-Charge Stanley Meador said authorities spent days searching by foot, boat and in the water for any leads.