The investigation led to charges against 20 members of the gang including distribution of methamphetamine. Three of the federal defendants were already in custody prior to Tuesday's operation.
Agents also seized drugs including methamphetamine and weapons.
"This is one of our larger operations and a very significant case for the city of Los Angeles," said FBI agent Timothy Delaney.
Agents say they took down the head of the gang's criminal money-making enterprise when they arrested 35-year-old Thomas "Big Boy" Rodriguez.
"This was not a street round-up of low level criminals but rather targeting the higher ups in the organization," said Delaney.
Nine separate federal indictments unsealed Tuesday charged 14 people in the case.
The suspects are facing federal and state charges, including distribution of drugs methamphetamine and extortion.
Those charged in the federal indictments include Thomas "Big Boy" Rodriguez, 35, of Los Angeles, Jose "Dreamer" Rodriguez, 34, of Los Angeles, Jorge "Spike" Orellana, 34, of Los Angeles, Anival "Pantera" Orellana, 35, of Los Angeles, Juan "Duende" Garcia, 32, of Los Angeles, Rogelio "Sky" Lemus, 42, of Los Angeles, Elvis "Lil' Comando" Molina, 33, a fugitive, of Lynwood, Jose "Chema" Avelar, 38, of Los Angeles, Lazaro "Fino" Nunez, 28, of Los Angeles, Fabel "Spooky" Roque, 25, of Kansas City, Sandra Hernandez Chinchila, 40, of Valencia, Mario "Plucky" Morales, no age or city given, Luis "Lil' One" Vega, 29, no city given and Edwin "Directo" Castillo, 31, no city given.
Those facing stage charges include Santos "Payaso" Ventura, 30, of Los Angeles, Jonathan "Lento" Chavez, 25, of Los Angeles, Thomas "Lil Lonely" Linares, 30, of Los Angeles, Oscar Chavez, 28, of Los Angeles, and 21-year-old Ivan "Inocente" Castro.
Morales, Vega, Castillo and Castro were already in custody on unrelated charges.
Candi Pascual, was also taken into custody Tuesday based on a state bench warrant.
Seven children were also removed by the Department of Children and Family Services from the defendant's residences Tuesday.
Federal investigators say, for more than two years, undercover agents infiltrated the gang learning who the key players were and how they operated.
"During the course of the investigation, we bought narcotics, weapons and we conducted undercover transactions to target this gang to get up to the important leadership - the highest level out on their street," said Delaney.
The Mara Salvatrucha gang, or MS-13 gang, is a notorious violent gang that was born in the immigrant communities just west of downtown L.A.
It has spread its violence and drug dealing across the country and into Mexico and Central America. The MS-13 gang is estimated to have several thousand members, and is known for its brutality and strong ties to the Mexican Mafia.
If convicted of the charges, federal authorities say the suspects face prison sentences ranging from 10 years to life.