One indictment, unsealed Thursday, alleges that Gerrit Keats of Clearwater, Fla., threatened Tygart via interstate communication in October.
The other, unsealed Friday, makes the same charge against Robert Hutchins of Sandy, Utah.
That indictment says Hutchins made the threat last Aug. 23, the same day Armstrong announced he wasn't going to fight the USADA sanctions for doping. "I have been subjected to a two-year federal criminal investigation followed by Travis Tygart's unconstitutional witch hunt," the cyclist said in a letter to the agency.
Keats was arrested Thursday in Clearwater and Hutchins on Tuesday in Salt Lake City. Both are scheduled to make appearances in federal court in Denver on July 29.
Making threats via interstate commerce carries up to a five-year prison sentence and a $250,000 fine.
A woman in the driveway of Keats' home, who refused to identify herself, said that neither he nor the family would talk. Public records identify Keats as a urologist born in 1941 with a clear and active medical license.
No one answered the phone at a number listed in public records for Hutchins.
Shortly after Armstrong said he wouldn't fight the USADA sanctions, Tygart revealed he had received death threats and was asking the FBI to investigate.
In an interview with "60 Minutes" following the Armstrong penalties, Tygart said the death threats came anonymously via emails and letters. Asked if he remembered any specific threats, Tygart said, "The worst was probably puttin' a bullet in my head."
When news of the arrests went public, USADA chairman Edwin Moses released a statement thanking the FBI and U.S. attorney's office for handling the case.
"We respect the judicial process and will continue to focus on our mission to protect the rights of clean athletes and the integrity of sport," Moses said.
In August, USADA handed Armstrong a lifetime ban and stripped all seven of his Tour de France titles for running what Tygart called "the most sophisticated, professionalized and successful doping program that sport has ever seen."
Since then, Armstrong has admitted to doping and stepped down from the Livestrong Foundation, which raised hundreds of millions of dollars for cancer research based largely on the cyclist's popularity. Armstrong overcame testicular cancer before winning his first Tour de France and used his story as an inspiration for others battling cancer.
Associated Press writers Paul Foy in Salt Lake City and Tamara Lush in Tampa, Fla., contributed to this report.