Carlos Guerrero, 45, was arrested at his Boonville residence Thursday, sheriff's Capt. Tracey Stuart said.
Guerrero was booked at 9 p.m. Thursday in the Napa County Jail on suspicion of possession of a controlled substance, cultivation of marijuana, possession of firearms and possession of firearms by a prohibited person, Stuart said.
"We believe he was involved in the marijuana grow," Stuart said.
Napa Special Investigations Bureau agents found a marijuana growing operation containing 3,000 immature pot plants about 2 feet tall and the bodies of the two men in the rural hills west of Rutherford.
The narcotics agents eradicated the garden, concealed by natural vegetation, on Wednesday, Stuart said.
The identities of the homicide victims have not been released. Stuart said the Napa County Major Crimes Investigation Team and other agencies hope to make more arrests in the case.
The marijuana was growing without the knowledge or consent of the private property owner and the homicide victims are not related to the property owner, Stuart said.