Tomas Medina Caracas of Farc was wanted by the US on cocaine-trafficking charges.
It is the only remaining Colombian gang to control the trade from the cultivation of coca plants to the production of cocaine and its exportation.
Montoya had been in a bitter turf war with the Norte de Valle cartel’s other leader, Wilber Varela, also known as “Jabon” (soap) and reported to be living in Venezuela.
Hundreds of people have been killed in battles between their rival armed militias along Colombia’s Pacific coast.
A US indictment filed in 2004 against Montoya and Varela said that in the previous 14 years their cartel had exported more than 500 metric tonnes of cocaine worth more than $10bn from Colombia to Mexico and ultimately to the United States for resale.
Montoya’s brother, Eugenio Montoya, was captured in Colombia in January.
Another top Montoya associate, Juan Carlos Ramirez Abadia, was captured in Brazil last month. It was unclear however, whether that arrest led to Montoya’s capture.
Monday’s capture comes during a scandal in which high level military officers are accused of taking bribes to protect Montoya.
Since taking office in 2002, Alvaro Uribe, Colombia’s president and a US ally, has approved the extradition of more than 540 Colombians to the United States, the majority on drug-trafficking charges.
For his aggressive stance, the United States has awarded Colombia with more than $700m in annual anti-drugs and military aid.
However, most of those extradited are suspected of being low or mid-level drug traffickers.
High-profile extraditions have included Gilberto and Miguel Rodriguez Orejuela, brothers who helped found the Cali cartel.
Colombia is the source of 90 per cent of the cocaine entering the United States. Supply has remained robust despite record extraditions and eradication of coca crops.