David K Reinke, 52, killed the rhino in 2009 with the blessing of the Namibian government. He argued that the killing was an act of "conservation hunting" because he was culling an elderly rhino that was unable to reproduce but could still aggressively crowd out fertile rivals.
But the decision angers wildlife supporters, who worry it sets a dangerous precedent encouraging trophy hunters to kill endangered animals.
"My desire is to help save the rhino through a scientific method approved by the United States and other agencies," Reinke said.
The US government has listed the black rhinoceros as endangered, making it illegal to import the animal dead or alive except for scientific purposes or if doing so enhances the species' survival.
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Other species of rhino, including the northern white rhinoceros, are protected as well.
The Fish and Wildlife Service said last month it granted Reinke's permit "in recognition of the role that well-managed, limited sport hunting plays" in the recovery of the black rhino in Namibia. The country allows five male black rhinos that are too old to reproduce to be shot each year, the service said.
"The removal of limited numbers of males has been shown to contribute to overall population growth in some areas by reducing fighting injuries and deaths among males, decreasing juvenile mortality and shortening calving intervals," the service said in a statement.
All black rhinos in Namibia are marked on their ears so officials can identify them and select which ones are appropriate for hunting. Reinke's target was Rhino bull No 27, which Namibian officials had monitored since it was brought to Waterberg Plateau National Park in 1981.