The president said Fito was in the custody of special military forces fighting narcotics trafficking.
The army and police reported that he was captured during an operation in the city of Manta, a fishing port in the western part of the country considered a stronghold for his gang.
Cartel terror campaign
Ecuador, once a peaceful haven between the world’s two top cocaine exporters, Colombia and Peru, has seen violence erupt in recent years as enemy gangs vie for control and establish ties to Mexican and Colombian cartels.
Macias Villamar is the leader of Los Choneros, the leading criminal gang in a country plagued by organised crime.
Gang wars largely play out inside the country’s prisons, where Macias Villamar wielded immense control.
He had been held since 2011, serving a 34-year sentence for organised crime, drug trafficking and murder.
When he escaped, he was also considered a suspect in ordering the assassination of presidential candidate and anti-corruption crusader Fernando Villavicencio.
In the hours after his escape, prison riots broke out and four police officers were taken hostage, with one forced to read a threatening message to Noboa.
Armed men wearing balaclavas took over a television station during a live broadcast, forcing the terrified crew to the ground and firing shots.
Soon after, Noboa announced the country was in a state of “internal armed conflict” and ordered the military and tanks into the streets to “neutralise” the gangs.
US prosecutors allege Macias Villamar’s gang worked with Mexico’s Sinaloa cartel to control key drug trafficking routes between South America and the US.
Ecuador’s Government had offered a US$1 million (NZ$1.65m) reward for information leading to his capture.
If convicted, he faces life in prison.
-Agence France-Presse