Gadahn, also known as Azzam al-Amriki and Azzam the American, was indicted by a federal grand jury in Santa Ana, California, for treason and supporting a terrorist organisation, the US Justice Department announced.
"A charge of treason is exceptionally severe, and it is not one we bring lightly," said Deputy US Attorney General Paul McNulty.
"But this is the right case for this charge" which carries a maximum penalty of death, Mr McNulty said.
Gadahn, 28, a native of southern California, has appeared in several videotapes for al-Qaeda since 2004, attacking the United States and praising the men who carried out the September 11, 2001 attacks on New York and Washington.
The tape in which he named Melbourne as a potential terrorist target was released by al-Qaeda in September last year.
"Adam Gadahn is an American citizen who made a choice. He chose to join our enemy and to provide it with aid and comfort by acting as a propagandist for al-Qaeda," Mr McNulty said.
Gadahn is believed to be outside the US and has been added to the Federal Bureau of Investigation's list of most wanted terrorists.