Carlos Holguin, the Colombian government, Miguel's capture was important not just because of drug-trafficking but because he and his brother, Victor, had created an armed group.
The arrest is part of a crackdown on cocaine smuggling rings run by former right-wing paramilitaries.
The brothers reportedly ran an operation called Los Mellizos (The Twins), and were considered to be Colombia's top drug traffickers.
Mejia and his brother Victor allegedly started off by trafficking cocaine before joining Colombia's paramilitary groups.
When the paramilitaries surrendered under a government brokered deal, the two brothers went on the run.
A US court issued extradition warrants for the two in 2004, claiming at the time they had shipped almost 70 tonnes of cocaine in just two years.
Alvaro Uribe, the Colombian president, has called on police to bring down the Mejia organisation, which is thought to contain dozens of smugglers and hired killers.