If convicted of the charge, Hutchins, 60, faces up to five years in prison and a $250,000 fine.
A second man, Gerrit Keats of Clearwater, Fla., faces the same charges in a separate case.
Hutchins allegedly made the threat days after a federal judge in Texas dismissed Armstrong's lawsuit against USADA, and as the cyclist opted not to fight USADA sanctions for doping violations and his attempts to cover up those actions.
In a statement released Aug. 23, 2012, Armstrong said he had been "subjected to a two-year federal criminal investigation followed by Travis Tygart's unconstitutional witch hunt. The toll this has taken on my family, and my work for our foundation and on me leads me to where I am today finished with this nonsense."
A day later, USADA announced Armstrong's lifetime ban from cycling and disqualification of his results beginning Aug. 1, 1998. Shortly afterward, Tygart revealed he had received death threats and asked the FBI to investigate. In an interview with "60 Minutes" following the Armstrong penalties, Tygart said 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."
In January 2013, Armstrong admitted doping during a televised interview with Oprah Winfrey.
"The information regarding the death threats directly received by USADA was referred to the appropriate federal law enforcement officials," said Edwin C. Moses, USADA board chairman, in a statement released to The Salt Lake Tribune. "We are grateful to the FBI and the U.S. Attorney's Office for handling this matter in accordance with the federal laws that are in place to protect the security and safety of citizens in this country. 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."
The Associated Press contributed to this story.