Some 179 people were arrested across Europe and the US, and 500kg (1,102lb) of drugs and 64 guns confiscated.
It ends the "golden age" of these underground marketplaces, Europol said.
"The hidden internet is no longer hidden", said Edvardas Sileris, head of Europol's cyber-crime centre.
The operation, known as DisrupTor, was a joint effort between the Department of Justice and Europol. It is believed that the criminals engaged in tens of thousands of sales of illicit goods and services across the US and Europe.