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.
The operation also saw the seizure of Bitcoins worth approximately $1m (£632,000).
"Today we have demonstrated that, together, we are able to efficiently remove vital criminal infrastructures that are supporting serious organised crime," said Troels Oerting, head of Europol's European cybercrime centre.
"And we are not 'just' removing these services from the open internet; this time we have also hit services on the dark net using Tor where, for a long time, criminals have considered themselves beyond reach," he added.
The BBC understands that the raid represented both a technological breakthrough - with police using new techniques to track down the physical location of dark net servers - as well as seeing an unprecedented level of international co-operation among law enforcement agencies.
The so-called deep web - the anonymous part of the internet - is estimated to be anything up to 500 times the size of the surface web.
Within that experts refer to the dark net - the part of the network which Tor operates on. There are approximately three million Tor users but the number of sites may be smaller.
Alan Woodward, a security consultant who advises Europol, said that the shutdown represents a new era in the fight against cybercrime.
"Tor has long been considered beyond the reach of law enforcement. This action proves that it is neither invisible nor untouchable," he said.
But, he added, it did not mean copycat sites would not spring up, or that the police had thrown light on the dark net.
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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.
The operation also saw the seizure of Bitcoins worth approximately $1m (£632,000).
"Today we have demonstrated that, together, we are able to efficiently remove vital criminal infrastructures that are supporting serious organised crime," said Troels Oerting, head of Europol's European cybercrime centre.
"And we are not 'just' removing these services from the open internet; this time we have also hit services on the dark net using Tor where, for a long time, criminals have considered themselves beyond reach," he added.
The BBC understands that the raid represented both a technological breakthrough - with police using new techniques to track down the physical location of dark net servers - as well as seeing an unprecedented level of international co-operation among law enforcement agencies.
The so-called deep web - the anonymous part of the internet - is estimated to be anything up to 500 times the size of the surface web.
Within that experts refer to the dark net - the part of the network which Tor operates on. There are approximately three million Tor users but the number of sites may be smaller.
Alan Woodward, a security consultant who advises Europol, said that the shutdown represents a new era in the fight against cybercrime.
"Tor has long been considered beyond the reach of law enforcement. This action proves that it is neither invisible nor untouchable," he said.
But, he added, it did not mean copycat sites would not spring up, or that the police had thrown light on the dark net.
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