A federal grand jury in Santa Ana on Wednesday issued the indictment against Adam Gadahn, 28, also known as Azzam al-Amriki, for treason and supporting a terrorist organisation, the department announced.
"A charge of treason is exceptionally severe, and it is not one we bring lightly," said Paul McNulty, deputy US attorney general.
Gadahn is believed to be overseas and is not in US custody.
The US justice department last brought treason charges during the second world war era, sources said.
Gadahn, who is also known on the videos as Azzam the American, has been involved in a propaganda campaign of al-Qaeda. Some of the videos have threatened attacks against the United States.
He converted to Islam from a Judeo-Christian family when he was 17 and a few years later moved to Pakistan. He previously was known as Adam Pearlman and grew up on a goat ranch outside Los Angeles.
The FBI has sought to question him since May 2004.
Besides treason, prosecutors have prepared other criminal charges against Gadahn, sources said.
The FBI has said that Gadahn attended al-Qaeda training camps in Afghanistan, that he has been associated with al-Qaeda's leaders and that he has done translations for al-Qaeda.