The US Attorney's Office in Nevada have charged Todd Davis, 44, and Joshua Keathley, 36, both of Lovelock, Nevada, over shootings that occurred on November 28 last year.
It is alleged they killed five wild horses on federally managed lands in northern Nevada.
The arrests were announced by Daniel Bogden, US Attorney for Nevada.
It is alleged Davis and Keathley maliciously caused the death and harassment of five wild free-roaming horses by shooting them in the Bureau of Land Management's Buckhorn horse management area in Northern Washoe County, Nevada.
Davis is employed by the Pershing County Water Conservation District in Lovelock. Keathley's employment is unknown.
Davis and Keathley are scheduled to make initial appearances in federal court on the charges on April 27.
If convicted, they face up to one year in prison and a $US100,000 fine.
The investigation is being conducted by the Bureau of Land Management's Office of Law Enforcement and Security California State Office in Redding, California, with help from the Lovelock Police Department, the Washoe County Sheriff's Office, the Washoe County Forensic Services Division, the Nevada Department of Wildlife, and the California Department of Fish and Game.
The Humane Society of the United States and the State of Nevada Commission for the Preservation of Wild Horses also contributed to the investigation.