The action came a day after a Manhattan judge approved the forfeiture of the bitcoins and the website, and three months after San Francisco entrepreneur Ross Ulbricht was arrested on charges he operated an online marketplace for illegal drugs, following a crackdown on the website.
He has pleaded not guilty to charges of narcotics trafficking, computer hacking and money laundering.
In a news release, US Attorney Preet Bharara said it was the largest forfeiture of bitcoins ever by the government. He called Silk Road "a global cyber business designed to broker criminal transactions."
The website is believed to have collected more than USD 1 billion in revenue from more than 100,000 customers.
"These bitcoins were forfeited not because they are bitcoins, but because they were, as the court found, the proceeds of crimes," Bharara said.
The prosecutor said yesterday investigators also seized more than USD 130 million worth of bitcoins from computer hardware belonging to Ulbricht, though US District Judge J Paul Oetken has not yet ruled whether those bitcoins must be forfeited.
Ulbricht, 29, has challenged the government's claims to that currency and its insistence that he operated online as Dread Pirate Roberts.
Oetken said Wednesday he was ordering the forfeiture of the USD 28 million of bitcoins and the website because no one had challenged the government's claims to those assets.
Ulbricht has remained imprisoned after a Manhattan magistrate judge cited "powerful evidence" that he sought the killings of individuals he believed would interfere with his business.
He is charged separately in federal court in Baltimore in an attempted murder-for-hire scheme.
A lawyer for Ulbricht did not immediately respond to a message for comment yesterday.