Mexican authorities found Trevino Morales -- known as "Z-40" -- as they intercepted a pickup truck on a dirt road in a town called Anahuac near the border of Tamaulipas and Nuevo Leon states.
Police said they arrested a total of three men during the raid. They were carrying $2 million in cash, three guns and multiple rounds. No shots were fired.
Eduardo Sanchez Hernandez, Mexico's Assistant Secretary of Media and Security, said the two other men were a bodyguard and an accountant.
Mexican authorities did not respond to questions regarding the United States involvement in the raid. The U.S. State Department had offered a $5 million reward for Trevino Morales.
Trevino Morales, 40, who reportedly took control of Los Zetas in October 2012, was taken into custody along with his two companions.