MS-13 is a transnational gang which was designated as a terrorist organisation by the US last year.
It was founded in Los Angeles during the 1980s, formed by immigrants who had fled El Salvador’s civil war, but its presence is now larger in Central America.
The attorney general’s office said “for years, this structure has operated systematically, instilling fear and grief in Salvadoran families”.
It said the charges against the 486 suspects people also included femicide and disappearances, adding that the crimes had impacted lives and limited the country’s economic and social development.
In addition, the accused are charged with “rebellion for attempting to maintain territorial control to establish a parallel state”, the office said.
It said 413 suspects were already in custody, while arrest warrants had been issued for 73 others who are being prosecuted in absentia.
El Salvador’s National Civil Police said it had developed research and monitoring efforts enabling it to “locate, capture, and document the criminal activity of the suspects”.
A controversial state of emergency, which expanded powers to arrest those suspected of gang affiliation or support and suspened some constitutional rights, has been in place in El Salvador since March 2022.
It has seen tens of thousands of suspected gang members arrested, but human rights groups have argued it has led to arbitrary detentions.
Legal changes in the country have also allowed for mass trials.