The undercover operation was called "Devil's Horns."
Early on Wednesday, federal agents and local police raided 35 locations. Most of them were in San Francisco, Richmond and Reno, Nevada. In total, 28 people were arrested.
Federal prosecutors say they are members of the notoriously violent Mara Salvatrucha, commonly known as the MS-13 gang.
Its origins are in Los Angeles. Many of its members cover themselves in tattoos. Federal investigators say most have ties to El Salvador.
"These enforcement actions are the culmination of three years of ice led criminal investigation resulting in the largest criminal indictment of MS-13 gang members in ICE's history," said U.S. ICE Investigations Director Marcy Forman.
U.S. Attorney Joe Russoniello, flanked by San Francisco District Attorney Kamala Harris and Police Chief Heather Fong, released details of the 52-count indictment against those arrested.
"This group of hoodlums, no other way to describe them, all in the name of some perverse loyalty, has engaged in some of the most vicious violent acts," said Russoniello.
The indictment says members of MS-13 in the Bay Area are divided into two groups. The turf for one is Richmond. The other is around 20th and Mission in San Francisco.
"They use violence, intimidation and fear in getting control of the turf and streets of San Francisco," said Forman.
The indictment says an export warehouse was set up in Richmond, where undercover agents bought stolen cars and guns from MS-13 members.
They also received assistance from the El Salvador national police. The raids were denounced by protestors outside the federal building.
"They don't have any proof they're gangsters, all of this is major racial profiling," said protestor Cinthya Munoz.
Immigration officials say that during the raids, 11 gang members were also taken into custody for possible immigration violations. They may face deportation.