Mexican marines detained the man on Wednesday near the border of the northern Mexican states of Sinaloa and Chihuahua, the public prosecution service said in a statement.
The suspect, Heraclio Osorio-Arellanes, is accused of carrying out along with other suspects the killing of US border patrol guard Brian Terry in December 2010.
Terry was killed on US soil while trying to intercept a group suspected of stealing drugs at the border.
Evidence found while investigating the killing indirectly brought to light a controversial arms-trafficking operation involving US authorities.
Mexico has notified the US government of the arrest with a view to extraditing the suspect to face trial in the United States, the prosecutors said.