Silk Road 2.0 and 400 other sites operating on the Tor network — a part of the internet unreachable via traditional search engines — have been shut down.
The joint operation between 16 European countries and the US saw 17 arrests.
Tor is home to thousands of illegal marketplaces, trading in drugs, child abuse images as well as sites for extremist groups.
Experts believe the shutdown represents a breakthrough for fighting cybercrime.
Among those arrested was Blake Benthall, who is said to have been behind Silk Road 2.0, a marketplace for the buying and selling of illegal drugs.
The site launched in October last year after the original Silk Road site was shut down and its alleged owner arrested, BBC informs.