Brian Richard Farrell is alleged to have told police that he was the "right hand man" of Silk Road 2.0 boss Defcon.
The arrest comes amid the trial of Ross Ulbricht, alleged to have run the original Silk Road.
The 26-year-old arrested in Seattle is alleged to be DoctorClu, the pseudonym for a senior administrator on the site.
He is charged with one count of conspiracy to distribute cocaine, heroin and methamphetamine.
Silk Road 2.0 sprang up in November 2013 and, until it was shut down in November 2014, is believed to have generated approximately $8m per month.
Blake Benthall, alleged to be the site's lead administrator Defcon, was arrested in San Francisco in November.
Dread Pirate Roberts
The trial of the man alleged to have run the original Silk Road is ongoing.
The charges against Mr Ulbricht include accusations of operating a continuing criminal enterprise, conspiring to commit narcotics trafficking, money laundering and computer hacking.
Prosecutors claim the site generated over a million untraceable drug deals and earned Mr Ulbricht $18m (£11.9m) in bitcoin commissions under the online pseudonym Dread Pirate Roberts.
He could face life in prison if found guilty on all charges.
He has denied all charges.
The defence set out to prove last week that the authorities have the wrong man in the dock, saying that Dread Pirate Roberts was in fact Mark Karpeles, the owner of the now-defunct Mt Gox Bitcoin exchange.
Karpeles has denied any connection to the Silk Road, and much of the evidence presented to the court - about the suspicions of one Department of Homeland Security special agent that Karpeles was the mastermind behind the Silk Road - has been ruled inadmissible by the judge as it was not based on "competent evidence".