Ross Ulbricht was arrested in a library in San Francisco. The affidavit did not say what he was doing there, but it did say he had his laptop with him, which may mean he was busy running what authorities say was a huge money laundering operation.
It's part of the so-called deep web, a site known as the Silk Road, where fictitious names and hard to track email are used to buy and sell illicit drugs.
The FBI says Ulbright was the mastermind behind the online drug black market. His pseudonym was Dread Pirate Roberts.
Ulbricht was once quoted as referring to his site as "anonymous Amazon.com."
Court documents say he generated tens of millions of dollars in commissions by being the middle man for the sale of heroin, cocaine, methamphetamine, LSD, and other drugs.
On Tuesday, the 29-year-old man was arrested at the Glen Park branch of the San Francisco Public Library.
Ulbricht was arraigned Wednesday in federal court on charges related to money laundering, drugs, and computer hacking.
The FBI says he lived with a friend in an apartment on Hickory Street in the city's Hayes Valley neighborhood.
During the investigation, the FBI says it made more than 100 undercover buys of drugs from Silk Road vendors.
Prosecutors say Ulbricht engaged in money laundering by using Bitcoins, a virtual currency, for the transactions.
According to court documents, over the past two years, Silk Road was used by several thousand drug dealers to sell $1.2 billion in illegal drugs which generated $80 million in commissions.
The criminal complaint also says Ulbricht was engaged in a murder-for-hire plot; that he solicited a Silk Road user to kill another user who was threatening to release the identities of thousands of other users. There was never any proof that the plot was ever carried out.