Thomas J. Leggs Jr. of Salisbury, 30, is charged with burglary and with kidnapping Sarah H. Foxwell, according to court documents.
A charging document says Leggs was the last person seen with Sarah.
Wicomico County Sheriff Mike Lewis said Sarah was last seen Tuesday night at her home on Maryland's Eastern Shore. A relative discovered she was missing early Wednesday while checking on Sarah and her 6-year-old sister.
"She wasn't in her room," Lewis said. He said there was no evidence of forced entry to the home where the girls live with their aunt, who is their legal guardian. Leggs is a former boyfriend of the aunt, officials said.
A "juvenile witness" awoke during the night Tuesday and saw Sarah leave the bedroom with "Tommy," and said he was wearing blue jeans, an orange jacket and white sneakers, the charging document says.
The statement of probable cause also says Sarah's aunt, Amy Fothergill, with whom Sarah lives, noticed that Sarah's green toothbrush was missing from the home. Deputies found a green toothbrush and a lollipop in a truck Leggs admitted driving. Leggs said he had been wearing jeans and white sneakers the previous night the same clothes he was wearing when police questioned him.
The sheriff said Leggs has been uncooperative and "of no assistance to our investigators."
Lewis said Thursday night police were still in search and rescue mode, and he said searches would continue throughout the night. "We have not lost hope," he said.
The sheriff said the department is encouraging hunters familiar with their hunting areas to start their own searches beginning at 7 a.m. on Christmas Day.
Dive teams searched a local pond Wednesday night, and scores of police officers from across the region scoured several square miles of dense woods on Christmas Eve. They brought in helicopters and dogs to aid their search.
Police also released a photograph of a 2003 Dodge Ram 1500 pickup used by Leggs and they asked anyone who may have seen the champagne/tan-colored vehicle to contact authorities.
Sarah is white, 4-foot-8 and weighs 78 pounds. She has brown hair and blue eyes. When she disappeared, she was wearing red fuzzy pajama bottoms with Christmas trees on them and a pink John Deere T-shirt.
Leggs is listed on the Maryland and Delaware sex offender registries. The Maryland listing notes that he is a child sex offender, but does not give details about his conviction.
Lewis said Leggs has been convicted of sex offense in Wicomico County and was charged Oct. 29 with fourth-degree burglary.
"He was developed as a suspect early on in the investigation before we were aware of his criminal background, but he does have a criminal history to include third- and fourth-degree sex offenses of small young females," Lewis said.
In 2001, Leggs was convicted in Delaware of rape for having sex with a victim who was 16 or 17, according to the Delaware registry. The registry describes his risk level as "high" and notes he is unemployed.
Leggs, who has been convicted of assault several times, also is awaiting trial on charges of burglary and destruction of property in Ocean City.