The D.C. Public Defender Service, which is representing Guandique, had no immediate comment on the new charges Thursday.
According to the new indictment, Guandique wrote a note to a witness identified only as "J.G." and had someone deliver it. The note threatened to kill J.G. or J.G.'s family if J.G. cooperated with law enforcement in the case against Guandique.
A second threatening letter was mailed to the witness by someone involved in the alleged conspiracy, according to the charges.
Levy, 24, had just completed an internship with the U.S. Bureau of Prisons when she disappeared after leaving her apartment in jogging clothes in May 2001. Her body was found a year later by a man walking a dog in Rock Creek Park.
The case, which stumped investigators for years, has been blamed for destroying the political career of former U.S. Rep. Gary Condit of California, who was romantically linked to Levy. Authorities questioned the Democrat, but he was never a suspect in her death.
When Guandique, 28, was charged this year with sexually assaulting and killing Levy, the illegal immigrant from El Salvador had been serving a 10-year sentence for separate assaults in Rock Creek Park.
Guandique's attorneys have criticized the lack of physical evidence in the case. The case rests in large part on two witnesses who said Guandique told them he was involved in Levy's killing.
The additional charges have delayed the trial, which had been scheduled to start next month.