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John Embree received his B.A. from the University of Hawaii in 1931, his M.A. from the University of Toronto in 1934 and his Ph.D from the University of Chicago in 1937. In 1935–36, as part of his doctoral thesis, he conducted field research in a rural area of Kumamoto on the southernmost Japanese island of Kyūshū. The study culminated in the seminal book Suye Mura: A Japanese Village, published in 1939 by the University of Chicago Press. His wife, Ella Lury Embree (later, Wiswell) conducted the research in Suye Mura alongside him, and subsequently published her own ethnographical work on the subject, The Women of Suye Mura.
John Embree served as Professor of Anthropology at the University of Hawaii in 1937–41 and during World War II in 1943–45. He was also Associate Professor of Anthropology and head of the Japanese area studies of the Civil Affairs Training School for the Far East which the War Department set up at the University of Chicago for the training of military government officers for Japan and the Occupied Areas. He was Associate Professor of Sociology and Research Associate of Anthropology at Yale from 1948 to 1950 and, later in the year, was appointed the university's Director of Southeast Asia Studies.
John Embree was 42 when, at year's end 1950, he and his only daughter, Clare, were killed in an accident.