Iyad Albattikhi, a 28-year-old divorcee, of Dickson Road, Blackpool, is charged with murder. Mohammed Raveshi, a 49-year-old bachelor of Hornby Road, Blackpool, is charged with assisting an offender.
After a day and a half of questioning, detectives formally charged the pair late last night and they were due to appear at Blackpool Magistrates' Court today.
Charlene, a pupil at St George's CE High School, went missing in November, 2003 and has not been seen since.
Forensic teams continued to comb the Funny Boyz takeaway, owned by Albattikhi, for evidence. Police have also searched the flat of the Jordanian-born defendant, which sits behind the fast-food outlet.
For a second day yesterday, teams of officers worked in a garage under the restaurant, drilling and digging for clues.
Iranian-born Raveshi, a property landlord who used to work for Social Services, was arrested in swoops on Tuesday.
Det Supt Paul Buschini said: "The searches at Funny Boyz and Hornby Road, will be concluded either today or early tomorrow. Some samples have been taken away for analysis."
A third man, also arrested in the co-ordinated operation on Tuesday morning, has been released on police bail pending further inquiries.