The charges were part of an 18-count indictment unveiled against Out of Africa Adventurous Safaris, as part of a multi-year investigation by the US Fish and Wildlife Service into wildlife trafficking crimes, known as Operation Crash.
Dawie Groenewald, 46, and his brother, Janneman Groenewald, 44, are also charged with mail fraud and violating the Lacey Act, which makes it a crime to sell products from illegal animal hunts.
Documents filed in federal court describe 11 rhino hunts that took place on the suspects' property in Limpopo Province in South Africa.
"The fact that these defendants allegedly used American hunters to execute this scheme, killing 11 critically endangered African rhinos, is appalling enough, but not as appalling as the brutal tactics that have been employed," he told reporters.
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"In one case, a horn was butchered off of a live tranquilized rhinoceros with a chainsaw."
Another rhino "had to be shot and killed after being repeatedly wounded by a bow," according to the indictment.
The hunts were illegal because the suspects did not obtain the necessary permits, US officials said. The American hunters who took part have not been charged.
The US Justice Department alleges that the Groenewald brothers recruited American hunters at conventions and gun shows, and sold them hunting trips at their ranch in Mussina, South Africa.
Hunters paid between USD 3,500 and USD 15,000 for the opportunity.
The South African men allegedly told US hunters that a particular rhino had to be killed because it was a problem to the herd.
"These defendants tricked, lied and defrauded American citizens in order to profit from these illegal rhinoceros hunts," said US Attorney George Beck of Alabama.