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NEW YORK — Michael D. Coe, a Yale anthropologist who devoted his career to proving that the ancient Maya incubated an elaborate written language that had previously been undervalued by many scholars, died of a stroke Sept 25 in a New Haven hospital. He was 90.

Dr. Coe was instrumental in deciphering the Maya script and in translating and validating the authenticity of what became known as the Grolier Codex — a document found in a Mexican cave that was believed to have been written around the 13th century on fig bark. It is considered the earliest existing manuscript in the Americas.

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First exhibited at the Grolier Club in Manhattan in 1971, it is one of only four written Maya works known to have survived marauding Spanish conquistadors and purges by Roman Catholic priests.

Dr. Coe defied contemporary critics who believed that the Maya hieroglyphics had been randomly inscribed and did not represent a recorded language. Instead, he embraced a discovery by the Soviet scholar Yuri Knorozov, who deciphered phonetic syllables in the Maya writing system, which allowed the texts to be read and spoken in their original language as well as translated.

Dr. Coe spent much of his career exploring the written language, paintings, and origins of societies that flourished in Mexico and Central America before the Spanish arrived in the early 16th century. He wrote of their invasion, “No imperial conquest has ever been so total, or a great people so shattered.”

But, in “Breaking the Maya Code” (1992), he theorized that anthropologists had not given the Maya adequate credit for their linguistic advances because of what he called “quasi-racism.”

Dr. Coe mined classical texts, probed dig sites with modern technological tools, and popularized the emerging field of ecological archeology, which studies how ancient civilizations related to their environment.

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He was also regarded as a champion of the Olmec civilization, which predated the Maya by about 2,100 years. He found and salvaged many of the Olmec’s enormous basalt sculptures of human heads and argued that the Olmecs were the “mother culture” of Mesoamerica.

“He was always willing to take unpopular positions and prove them correct,” said Richard A. Diehl, professor emeritus of anthropology at the University of Alabama, who was a graduate student when he began working with Dr. Coe in 1966.

Reviewing “The Art of the Maya Scribe” (1997), which Dr. Coe wrote with Justin Kerr, Souren Melikian said in The International Herald Tribune, “The moment you open the book, you feel you have been handed keys to hitherto impenetrable secrets.”

Dr. Coe’s other books included “Mexico: From the Olmecs to the Aztecs” (1962), “The Maya” (1966), “The Maya Scribe and His World” (1973), and a memoir, “Final Report: An Archaeologist Excavates His Past” (2006). His book “Breaking the Maya Code” inspired a 2008 documentary.

After his wife, Sophie D. Coe, an anthropologist and food historian, died of cancer in 1994, Dr. Coe fulfilled his promise to finish her book “The True History of Chocolate,’’ in 1996.

Michael Douglas Coe was born on May 14, 1929, in Manhattan and was raised on Planting Fields, a 400-acre estate in Oyster Bay, on Long Island; it is now a state park. His father, William Rogers Coe, was vice president of the Virginian Railroad and a grandson of Henry Huttleston Rogers, a founder of Standard Oil. His mother, Clover, was a dress designer.

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Michael originally hoped to become a writer. But at St. Paul’s School in Concord, N.H., as a prize for his religious studies work, he won a copy of “The Book of a Thousand Tongues,” which translated the gospel of St. Mark into multiple languages. The book propelled him toward the study of anthropology.

“It hooked me from the beginning,” he said in a memoir.

After graduating from St. Paul’s, he enrolled at Harvard, where, he later said, he couldn’t find a relevant creative writing course. Then, while on a family vacation to the Yucatán, he toured the ancient Maya ruins at Chichen Itza and was mesmerized by the mysterious wall paintings and hieroglyphs. When he returned to college, he switched his major from English literature to anthropology. He graduated in 1950.

A Harvard anthropology professor recruited him to the front lines of the Cold War. He went to work for a business organization in Taiwan that was actually a front for the Central Intelligence Agency, which was trying to subvert the nascent Communist regime in Beijing.

He completed his doctorate in anthropology at Harvard.

He married Sophie Dobzhansky, a Radcliffe anthropology student and the daughter of the Russian émigré geneticist Theodosius Dobzhansky, in 1955. He leaves three sons, Andrew, Nicholas, and Peter; two daughters, Sarah and Natalie Coe; and six grandchildren.

While he was best known for his work in the Americas, Dr. Coe also conducted comparative studies of ancient tropical forest societies, including the Khmer civilization in Cambodia.

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In a 1978 essay, he presented a cautionary tale of what an archeologist might erroneously conclude thousands of years in the future about the origins, chronology, and architecture of the three churches on the historic New Haven Green, based only on an examination of their remains. He suggested that those hypothetical findings ought to humble his contemporaries who overconfidently draw conclusions about ancient civilizations.

“I notice that archeologists who come up with neat models for prehistoric cultural events seem to feel that they are presenting us with some sort of reality,” he wrote. “It is lucky for these scholars that the long-dead subjects of their study cannot now contradict them.”