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Wilber was a principal architect of the CIA project "Operation Ajax", a successful plot to overthrow the government of Iranian Prime Minister Mohammad Mossadeq. The plot replaced Iran's first democratically elected Prime Minister with General Fazlollah Zahedi; the government fell back into the hands of its disempowered Mohammad Reza Shah Pahlavi, who had supported the coup. He later ordered the deaths of thousands of Iranians through SAVAK, the Shah's tightly controlled secret police, in his following regime.
Wilber served as a United States intelligence officer with the Office of Strategic Services (OSS), and was an active participant in the power struggles of nations, especially during the rivalry between the United States and the Soviet Union in Iran after World War II.
In addition to orchestrating the coup in Iran to benefit oil barons in Britain and the United States, in his spare time, Wilber wrote histories, travelogues and commentaries on Iran, Afghanistan and Sri Lanka. He was considered an authority on ancient Persia.
Wilber studied the ancient and modern Middle East. He received his A.B. (1929), M.F.A., and Ph.D. (1949) from Princeton University, where he was the first student to receive a doctorate in architectural history.
In 1939 Wilber married Margaret Patterson Surre; they had two daughters, Sara Wilber Cohen and Margaret Newton Wilber, who later changed her name to Valentine Margaret Wilbur because of her February 14 birthday.
His book Iran Past and Present, was published in nine editions. Wilber collected oriental rugs, and was president of the Princeton Rug Society for many years. He spent forty years in the Middle East.
His memoir, which partially recounts his role in the coup, is Adventures in the Middle East and Iran, Past and Present and Iran Past.
In August 2003, California State University Economics Professor Sasan Fayazmanesh, an Iranian expatriate, wrote:
On April 16, 2000, The New York Times broke what its writer, James Risen, called the US's "stony silence" by devoting a number of pages to publishing parts of a still classified document on the "secret history" of the 1953 coup. The history was written by one Donald N. Wilbur, an expert in Persian architecture and one of the "leading planners" of the operation "TP-Ajax."
The report chronicled gruesome details of the events in 1953: how, by spending a meager sum of $1 million, the CIA "stirred up considerable unrest in Iran, giving Iranians a clear choice between instability and supporting the shah"; how it brought "the largest mobs" into the street; how it "began disseminating 'gray propaganda' passing out anti-Mossadegh cartoons in the streets and planting unflattering articles in local press"; how the CIA's "Iranian operatives pretending to be Communists threatened Muslim leaders with 'savage punishment if they opposed Mossadegh'"; how the "house of at least one prominent Muslim was bombed by CIA agents posing as Communists"; how the CIA tried to "orchestrate a call for a holy war against Communism"; how on August 19 "a journalist who was one of the agency's most important Iranian agents led a crowd toward Parliament, inciting people to set fire to the offices of a newspaper owned by Dr. Mossadegh's foreign minister"; how American agents swung "security forces to the side of the demonstrators"; how the shah's disbanded "Imperial Guard seized trucks and drove through the street"; how by "10:15 there were pro-shah truckloads of military personnel at all main squares"; how the "pro-shah speakers went on the air, broadcasting the coups' success and reading royal decrees"; how at the US embassy, "CIA officers were elated, and Mr. Roosevelt got General Zahedi out of hiding" and found him a tank that "drove him to the radio station, where he spoke to the nation"; and, finally, how "Dr. Mossadegh and other government officials were rounded up, while officers supporting General Zahedi placed 'unknown supports of TP-Ajax' in command of all units of Tehran garrison."
"It was a day that should have never ended," Risen quotes Wilber as saying, for "it carried with it such a sense of excitement, of satisfaction and of jubilation that it is doubtful whether any other can come up to it." 
Wilber is the author of articles and books, including:
- The Islamic Architecture of Iran and Turan: The Timurid Period (with Lisa Golombek, Princeton University Press, 2 vols.)
- Iran Past and Present (Princeton University Press)
- The Architecture of Islamic Iran: The Il Khanid Period (Princeton University Press)
- Persian Gardens and Garden Pavilions (Dumbarton Oaks)
- Pakistan Yesterday and Today (Holt, Rinehart and Winston)
- Persepolis: The Archaeology of Parsa, Seat of the Persian Kings (The Darwin Press, Inc.)
- The Land and People of Ceylon (J. B. Lippincott Company)
- Contemporary Iran (Frederick A. Praeger)
- Adventures in the Middle East: Excursions and Incursions (The Darwin Press, Inc.)
- Afghanistan its people its society its culture (HRAF PRESS)
- Zinn, Howard & Buhle, Paul. A People's History of American Empire. New York: Metropolitan Books, 2008. p. 235