His death was confirmed by his editor, Robert Weil.

Like his mentor and fellow atheist, the Harvard historian Perry Miller, Professor Morgan found his richest material in the religious thought of Puritan New England and endless fascination in the theological debates and spiritual struggles of men like John Winthrop, Roger Williams and Ezra Stiles.

"I think that any group of people who have a system of belief that covers practically everything, and who act upon it, are bound to be interesting to any scholar," he said in a 1987 interview with The William and Mary Quarterly.

His elegantly written, succinct biographies and studies of early New England, respected by specialists but accessible to undergraduates, became required reading for several generations of college students.

"As a historian of colonial and revolutionary America, he was one of the giants of his generation, and a writer who could well have commanded a larger nonacademic audience than I suspect he received," said Pauline Maier, a professor of American history at the Massachusetts Institute of Technology. "He characteristically took on big issues and had a knack for conveying complex, sophisticated truths in a way that made them seem, if not simple, at least easily understandable."

Professor Morgan's book "The Puritan Dilemma: The Story of John Winthrop" (1958) was for decades one of the most widely assigned texts in survey courses on American history. His "Visible Saints: The History of a Puritan Idea" (1963) showed his unmatched talent for mining primary sources to illuminate an important concept, in this case the change in understanding among New Englanders of what it meant to be the member of a church.

Professor Morgan later became intrigued by colonial Virginia, a slaveholding society that produced some of America's most sophisticated theoreticians of human freedom. This paradox was the subject of "American Slavery, American Freedom: The Ordeal of Colonial Virginia" (1975), which won the Francis Parkman Prize in 1976. "Inventing the People: The Rise of Popular Sovereignty in England and America" (1988) won the Bancroft Prize in American History in 1989.

A prolific writer well into his 90s, Professor Morgan made a belated appearance on The New York Times's best-seller list in 2002 with the lively, eminently readable "Benjamin Franklin."

Based almost entirely on primary documents in Yale's collection of Franklin papers, it presented a more vigorous, impassioned founding father than the traditional portrait of, as he wrote, "a comfortable old gentleman staring out at the world over his half-glasses with benevolent comprehension of everything in it."

"My view has always been that an analysis of historical developments should be embodied in narrative," Professor Morgan told The Yale Bulletin and Calendar in 2001. "A historian should not be didactic — that is a word that makes my blood run cold."

Edmund Sears Morgan was born on Jan. 17, 1916, in Minneapolis. His father, Edmund Morris Morgan, was an expert on the law of evidence and served as chairman of the committee that drafted the first uniform code of military justice for the armed forces in 1948.

Edmund grew up in Arlington, Mass., where the family moved after his father began teaching at Harvard's law school. He enrolled in Harvard intending to study English history and literature, but after taking a course in American literature with F. O. Matthiessen, he changed to the newly offered major of American history and literature, with Perry Miller as his tutor. He received a bachelor's degree in 1937, and, at the urging of the jurist Felix Frankfurter, a family friend, he attended lectures at the London School of Economics.

In 1942, he completed a doctorate in Harvard's new program on the history of American civilization under Professor Miller's supervision. His dissertation, on the domestic life of the Puritans, became his first book: "The Puritan Family: Religion and Domestic Relations in 17th-Century New England" (1944).