The indictment comes four months after federal prosecutors first filed a complaint against Ulbricht and arrested him in California. The original complaint did not include the "continuing criminal enterprise" clause.
A lawyer for Ulbricht, Joshua Dratel, said his client would plead not guilty at an arraignment scheduled for Friday.
"The indictment was expected and does not contain any new factual allegations," Dratel said in a statement, according to The Associated Press.
Federal prosecutors have previously said that the Silk Road operation generated more than $1.2 billion in sales, but that amount was calculated based on the website’s sole usable currency — bitcoin, a semi-anonymous, online-only method of exchange.
According to the government, Silk Road made sales worth 9.5 million bitcoins, while Ulbricht himself is alleged to have pocketed 600,000 bitcoins in commissions. Authorities have seized only around 174,000 bitcoins believed to be connected to Silk Road. On Tuesday night, one bitcoin was worth $928 on one of the world’s largest bitcoin exchanges, Mt. Gox.
The continuing criminal enterprise statute has previously been used against some of the world’s most notorious criminals. In the 1990s, prosecutors leveled the charge against Larry Hoover, the chief of Chicago’s Gangster Disciples. In 2007, it was used against the leader of the Arellano-Felix Organization, a Tijuana-based drug cartel that kidnapped, tortured and murdered opponents while earning hundreds of millions of dollars.
The indictment also accused Ulbricht - who prosecutors say operated under the online alias Dread Pirate Roberts - of conspiracy to commit narcotics trafficking, computer hacking and money laundering, and federal prosecutors in Maryland have filed their own case alleging that Ulbricht tried to hire someone to murder one of his Silk Road deputies, who he believed was co-operating with the police.
Ulbricht was arrested by agents from the Federal Bureau of Investigation at a branch of the San Francisco Public Library in the family-friendly Glen Park neighborhood on Oct. 1 while logged into the Silk Road as an administrator, prosecutors have alleged. The site was removed from the Internet the same day, although a new Silk Road — also available only by using the anonymizing Tor web browser — has since sprung up.
Since Ulbricht’s arrest, at least four high-level employees of the Silk Road have been arrested or charged, likely indicating the deep access federal authorities gained to the site’s inner workings during their two-year investigation.
In November, former administrator Curtis Clark Green — known by his Silk Road aliases “Flush” and “chronicpain” — pleaded guilty in a Maryland federal court to conspiracy to distribute cocaine after being caught in a sting in January 2013.
In December, federal prosecutors in Manhattan unsealed indictments against three other men — Andrew Michael Jones, Peter Philip Nash and Gary Davis. Jones and Nash allegedly worked as administrators, while Davis served as a moderator on Silk Road’s user forums.
Davis is reportedly free on bail in Ireland, while Nash is in custody in Australia. Jones was arrested on Dec. 19 in Virginia and freed on a $1 million bond secured by his parents’ home and $250,000 retirement account, according to court records. His travel was ordered restricted to the areas of New York and Virginia where he lives and will attend court proceedings.