Booth most recently was the U.S. ambassador to Ethiopia.
"Ambassador Booth is one of America's most experienced diplomats, with broad experience helping promote peace and prevent conflict across Africa," the president said in a statement released by the White House.
"With his considerable diplomatic talents, deep knowledge of the continent and unwavering determination, I am confident that Ambassador Booth will advance U.S. interests in pursuing a durable and lasting peace between and within Sudan and South Sudan."
Obama said Booth will head up U.S. diplomatic efforts to get Sudan and South Sudan to implement agreements reached last September and resolve their border and other disputes.
"He will also lead our efforts to bring the conflicts in Blue Nile, Southern Kordofan and Darfur to a peaceful end, and to promote inclusive governance and full respect for human rights in both states," the president said.
"Much work remains, but we know that when the governments of Sudan and South Sudan show political courage and put the interests of their people first, peace and progress are possible."