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.
They allowed guns to be trafficked across the border to Mexico in the hope of tracking them, but lost trace of some of the weapons after gangs got hold of them.
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.
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