In Fairfax County, Virginia on Monday, Jesse Matthew, 32, was also indicted on charges of attempted capital murder.
Mr Matthew is being held in connection with Ms Graham's disappearance on 13 September.
On Saturday, authorities discovered a body which may be Ms Graham's in Albemarle County.
In the newest charges, Virginia officials have thus far declined to offer further details regarding the investigation and victim, a 24-year-old woman abducted from suburban Washington DC in 2005.
|Hannah Graham went missing after a night out|
Mr Matthew is currently being held in Charlottesville, Virginia, where he has been charged with abduction with intent to defile.
Ms Graham, 18, was last seen on 13 September, when she disappeared after an evening of drinking and socialising with friends.
She had been in her second year of study at the University of Virginia, where she was described as a bright student who got top marks in her exams.
She was born in Reading, southern England, and moved to the US with her parents at the age of five.
On Saturday, a body was discovered in an abandoned property in Albermarle County.
Charlottesville police chief Timothy J Longo earlier said officers had contacted Ms Graham's parents shortly after a search team found the body and made a preliminary identification.
Positive identification will only be made after a post-mortem is conducted by the state medical examiner, Detective Sgt James Mooney of the Charlottesville Police Department told local media.
Mr Matthew, a nursing assistant, was identified as a suspect soon after Ms Graham's disappearance.
Witnesses reported seeing a man matching his physical description drinking with Ms Graham on the night she went missing, and he appeared twice in CCTV footage walking alongside her, police said.
He was taken into custody by police in Galveston, Texas, 1,300 miles (2,092km) from where Ms Graham was last seen.
|Jesse Matthew was earlier charged in connection with |
Hannah Graham's September disappearance
Her body was found on a farm in Albemarle County three months after she went missing.
Ms Harrington's case has been linked by DNA evidence since 2012 to the rape of a woman in Fairfax, Virginia, who survived after a passer-by startled her attacker, the FBI says.
Good grief! This guy is an alleged monster. So, it appears more rape charges will be forth-coming.