Deadly drugs war
All but one of the defendants face up to life in prison if they are captured and convicted.
"Our intention is to indict these people, to get these people to the United States and to put them in jail for extended periods of time"
Eric Holder, US attorney-general
"Let me make something very, very clear here; these are not symbolic acts that we are taking today," Holder said.
"Our intention is to indict these people, to get these people to the United States and to put them in jail for extended periods of time."
Guzman is one of the biggest drugs barons in Mexico, where 13,000 people have died in a drugs war between state authorities and the cartels over the past three years.
He is accused, along with Ismael Zambada Garcia and Arturo Beltran Leyva, of running a drug-trafficking network in Mexico.
Vicente Carrillo Fuentes, the alleged head of the Juarez drug cartel, was also named as being indicted by US authorities.
Guzman leads the Sinaloa cartel, which is generally regarded as being the group most responsible for drugs-related violence across Mexico.
He escaped from a high-security jail in Mexico in 2001 before he could be extradited to the US, and he has since sought to expand his operations along the US-Mexico border.
Holder and Michele Leonhart, the acting head of the US Drug Enforcement Agency, said on Thursday that the US is offering a reward of up to $5m for information leading to the arrests of the Mexican drug cartel leaders.
About 90 per cent of the cocaine that comes into the United States is smuggled via Mexico, the DEA says.