The charges have been brought by courts in New York and Miami, which accuse the gang of exporting more than 73 tonnes of cocaine into the US since 2002.
Most of the 17 people charged are still at large, including gang leader Dairo Antonio Usuga David, known as Otoniel.
The United States says it will try to secure the extradition of the alleged Clan Usuga members.
The announcement of the indictments was made by President Juan Manuel Santos in Bogota, at a joint media conference with American officials.
"We will continue to act strongly against these criminals who poison our youth, who sow violence, who promote corruption not only in Colombia but across the world," said Mr Santos.
The US has previously offered up to $5m (Â£3.4m) for information leading to Otoniel's arrest.
Otoniel has been in charge since his brother, Juan de Dios, was killed on 1 January 2012 when police raided his New Year's Eve party.
The gang is mainly engaged in drug trafficking, but it has also been accused of extortion, illegal mining, forced disappearances and murder, says the BBC's Natalio Cosoy in Bogota.
Colombian police estimate the gang has some 2,000 active members.
Over the past five years, the security forces have captured 6,700 members of the group.
"Your operatives will continue to be dismantled; they will be captured and your government, our ally in Colombia, will work with us to secure your extradition," said Wifredo Ferrer, US attorney for the Southern District of Florida at the presidential palace in Bogota.
Clan Usuga operates in several countries in the region. Members have been arrested as far away as Argentina, Brazil, Honduras, Peru and Spain.
The United States has indicted 17 alleged members of one of Colombia's largest criminal gangs, Clan Usuga.