Assange was previously indicted in April on a single-count conspiracy to commit computer intrusion charge for his role coordinating with Manning.
The US Justice Department unveiled 17 new counts under the Espionage Act against WikiLeaks founder Assange.
One of the counts included in the superseding indictment includes a charge of conspiracy between Manning and and Assange to obtain receive and disclose national defense information in violation of Espionage Act, a rare charge for a person who has never served inside the US government. Most cases involving the theft of classified information have targeted government employees, like Manning, and not the people who publish the information itself.
The new indictment says Assange conspired with Manning to obtain and disclose classified national defence documents, including State Department cables and reports on the wars in Iraq and Afghanistan.
After spending years in the Ecuadorian embassy in London, Assange was evicted and arrested on a USA extradition warrant in April related to one charge regarding conspiracy to hack. It says his actions "risked serious harm" to the United States.
WikiLeaks, however, reacted to the news with a tweet saying it amounted to the "end of national security journalism and the first amendment".
In one such message, Manning allegedly tells Assange "i told you before, government/organizations cant control information... the harder they try, the more violently the information wants to get out".
Assange is now serving a jail sentence in the United Kingdom for breaching bail conditions and faces extradition.
"Julian Assange is no journalist", said Assistant Attorney General John Demers, the Justice Department's top national security official.
He and other officials said they only charged Assange with publishing a narrow subset of material that included the names of sources, including people who risked their lives talking to the United States government. "But Julian Assange is no journalist".