If sentenced, Dairo Antonio Usuga David will face mandatory minimum term of 20 years and up to life in prison.
The seizure of 4.3 tonnes of cocaine came at the end of an international investigation that resulted in arrest warrants being issued for 38 people in six countries.
Antonio Usuga David and his drug cartel Gulf Clan are accused of illegally bringing over 73 tonnes of cocaine into the US between 2003 and 2012.
A bombardment by government forces killed 23 dissident members of the demobilised Revolutionary Armed Forces of Colombia, or FARC, including commander Jorge Eliecer Jimenez, known as Arturo.
Colombia had offered a reward of up to about $800,000 (3 billion pesos) for information concerning Otoniel's whereabouts, while the US government had put up a reward of $5 million for help locating him.
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