Officials said the pair checked into the hotel at 6:11 a.m. Tuesday morning, apparently before Davis' mother reported her missing.
After reviewing surveillance video at the hotel, police identified the man with Davis as 29-year-old Mario Andrette McNeill.
Authorities said the connection between the girl and McNeill is unknown at this time.
Police said they want to reunite the child with her family and believe she is still alive. They also have upgraded an Amber Alert issued for her to nationwide.
Davis' father pleaded at the press conference for his daughter's safe return.
"Shaniya, if you are listening to daddy ... I miss you so much ... I'm not going to give up," Bradley Lockhart said.
Earlier Thursday, the Fayetteville Police Department announced the arrest of 30-year-old Clarence Coe after a witness said they saw him leaving the mobile home park where Davis lives with her in his car.
Police arrested Coe of Brookwood Ave. in Fayetteville just after 11 p.m. Wednesday. He is charged with first-degree kidnapping and remains in the Cumberland County Detention Center without bond.
Officials did not identify the witness or say what time Coe was allegedly seen with the girl.
Investigators also did not say how Coe knows the child or the Davis family, but they did say they don't believe it was a random abduction.
The manager of the Sleepy Hollow Mobile Home Park, where the Davis family lives, told ABC11 Eyewitness News that Coe is the boyfriend of Antoinette Davis, Shaniya's mother.
According to state records, Coe was recently released from prison after serving four months behind bars for assaulting a woman earlier this year. Coe also has previous breaking and entering and larceny convictions dating back several years.
Crime scene technicians have collected evidence from the home. Wednesday night, they found a blanket believed to belong to the child in a neighbor's outside trash can. Police say the neighbor, Andrea Moore, is not a suspect.
Since the investigation began, police have suspected foul play was involved. They said Thursday that Coe was a person of interest early on. A police spokesman wouldn't say Thursday if he was cooperating with detectives.
Anyone having any information on the current whereabouts' of Mario McNeill or Shaniya Davis is urged to contact the Fayetteville Police Department at 910-433-1856. To leave an anonymous tip, please contact Crime Stoppers at 910-483-8477.