Canadian Roger Thomas Clark is said to have been a key adviser for Silk Road creator Ross Ulbricht.
The US Department of Justice alleged that Mr Clark advised Ulbricht about the best way to run the site and how to evade the police.
The Silk Road website was shut down in late 2013 following raids by the FBI and other law enforcement agencies.
It was a marketplace sited on the dark web through which many people bought illegal drugs. In May this year Ross Ulbricht was sentenced to life in prison for creating and running the site.
The DoJ alleges that Mr Clark was a "high-ranking" operator on the Silk Road and was instrumental in helping Ulbricht run it. He gave advice about ways to improve the technology underpinning the site, boost sales and on the best way for Ulbricht to hide his real identity, said US authorities.
Mr Clark was paid "at least hundreds of thousands of dollars" for this advice, said the DoJ in a statement announcing the arrest.
"Clark may have thought residing in Thailand would keep him out of reach of US authorities, but our international partnerships have proven him wrong," said FBI assistant director Diego Rodriguez.
On the site and in other underground forums, Mr Clark is believed to have used several nicknames including "Variety Jones, "VJ", "Cimon" and "Plural of Mongoose".
Extradition proceedings have been started against Mr Clark to transfer him from a jail in Thailand to the US.
He faces charges of narcotics conspiracy and money laundering. If found guilty of both charges he could face 30 years in jail.
A man alleged to have helped run the notorious Silk Road drug marketplace has been arrested in Thailand.