Newton County Sheriff Ken Copeland said 24-year-old David Spears was arrested in the death of Rowan Ford.
"The stepfather was a possible suspect," Copeland told The Associated Press. "I will confirm that he has been arrested, as well as one of his friends."
Copeland said a 24-year-old man from Wheaton, in adjacent Barry County, was also arrested. Charges had not been filed as of Friday night.
Rowan's body was found on private land about 10 miles south of the girl's hometown of Stella, a village of about 200 people, Copeland said.
Authorities believe she was killed in adjacent Barry County and her body then taken to nearby McDonald County, he said.
Copeland referred questions to the Barry County sheriff, who did not immediately return a phone call.
Copeland had said earlier that authorities were still determining how the girl died.
"We know we have a homicide," Copeland said, declining to elaborate.
The McDonald County deputy who found the body had searched the area on his way to work after recalling that there was a cavern there, Copeland said. The FBI was gathering the evidence at the scene.
Stella Mayor Bill Alsop, who answered the phone at the family's home Friday, said the girl's mother was "pretty shook up" when Copeland came to the home that morning and told her the body was very likely Rowan's.
"He told her they found the body of the little girl, and they were 99 percent sure it was her daughter," Alsop said.
Rowan was reported missing after her mother, Colleen Spears, returned home early Nov. 3 from a night shift at a Wal-Mart.
David Spears told investigators that he and two male friends were with Rowan the night before until they went out around 10:45 p.m. He returned home around midnight but did not check on the girl, Copeland said.
David Spears also later told authorities that he called his mother sometime after 1 a.m. and asked to use her vehicle, Copeland has said. She took it to him about half an hour later, then stayed at his house while her son left in her vehicle for about 5½ hours, Copeland has said.
Copeland also has said that David Spears has not been able to explain what he did during that time.
David Spears declined to comment. He has been staying at his mother's house outside Stella since Rowan's disappearance.
"He's pretty torn up. He's extremely distraught. He's been crying quite a bit," his mother, Myrna Spears, said.
His mother declined to answer any questions about what happened that night. David Spears previously has said that it was wrong for him to leave the girl alone.