Michael D. Coe, an archaeologist and anthropologist who shined a light on ancient Mesoamerican civilizations, leading excavations in Guatemala and Mexico, helping decode Maya writing and art, and writing best-selling books that galvanized public interest in his field, died Sept. 25 at a hospital in New Haven, Conn. He was 90.

He suffered a stroke, said his son Andrew Coe, a writer and food historian.

Driven by a sense of ad­ven­ture, Dr. Coe worked as a CIA officer in Taiwan before beginning his archaeological career in Guatemala in the mid-1950s, excavating a site on the Pacific Ocean that was previously ignored — in part because of the sweltering heat and mosquitoes. He returned to the United States one Christmas and spent most of the holiday in bed recovering from malaria.

Later digging in the dirt of San Lorenzo, near the Gulf of Mexico in Veracruz, Dr. Coe unearthed colossal stone heads and monuments left behind by the Olmec, a civilization he helped date, tracing its roots back more than 3,000 years. He also deciphered the meaning of cryptic Maya ceramics and writing symbols, or glyphs, and drew attention to a bark-paper document known as the Grolier Codex, generally considered one of only four surviving Maya manuscripts, or codices.

“Mike was one of the greatest archaeologists of the 20th century and a peerless popularizer of our field,” said Stephen D. Houston, a fellow Maya scholar and chairman of the Brown University anthropology department.

In works such as “Mexico: From the Olmecs to the Aztecs” (1962), “The Maya” (1966) and “Breaking the Maya Code” (1992), Houston said, Dr. Coe “combined a fluency of expression with real learning and real accomplishment as a first-rank scholar on his own.”

Based at Yale University for 34 years before retiring in 1994, Dr. Coe taught thousands of students and wrote for an audience that ranged from academics and armchair historians to archaeological junkies and tourists to Mexico. “Breaking the Maya Code,” which chronicled the years-long effort to crack the Maya script (a mammoth undertaking aided by Dr. Coe and his wife, Sophie D. Coe, a food historian trained as an anthropologist), was adapted into a popular 2008 documentary and inspired a “Nova” program on public television.

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His early research also suggested that the Maya may have believed in an apocalyptic event at the end of their 5,125-year calendar cycle, in which “Armageddon would overtake the degenerate peoples of the world and all creation,” according to Dr. Coe.

Those lines, from his book “The Maya,” contributed to a pop-culture sensation in 2012, when New Age mystics spoke of a “Mayan prophecy” nearing fruition and hunkered down for the end of the world. Dr. Coe was said to have been mildly annoyed by all the fuss.

Coming of age in an era before most scholars were siloed in narrow academic disciplines, his work ranged far beyond the Maya: He was a scholar of Angkor Wat and the Khmer civilization in Southeast Asia, excavated a colonial-era fort near a farm he owned in the Berkshires of Massachusetts, and became a historian of fly-fishing, a hobby he pursued obsessively from Labrador to Siberia.

For a time, he accompanied his wife on trips to Europe, where she pored over 400-year-old texts while preparing a comprehensive history of chocolate. After Sophie was diagnosed with cancer in March 1994 (she died two months later), Dr. Coe promised to complete what became “The True History of Chocolate,” and was listed as junior author when it was published in 1996.

“It was the first book in the contemporary era, in English, that took chocolate as a serious field of study,” said Carla D. Martin , a Harvard lecturer and the founder and executive director of the Fine Cacao and Chocolate Institute.

Dr. Coe was perhaps an unlikely candidate for scholarly work. Raised in wealth and privilege on the Gold Coast of Long Island, he was the great-grandson of Standard Oil executive Henry Huttleston Rogers, a builder of the Virginian Railway, where Dr. Coe’s father was vice president.

He had initially planned to become a writer, studying English at Harvard before a visit to the Maya ruins of Chichen Itza steered him toward anthropology. Then a professor asked if he’d like to “work for the government in a really interesting capacity” — a suggestion that launched his brief career in the CIA.

According to “Legacy of Ashes,” a history of the agency by journalist Tim Weiner, Dr. Coe adopted a pseudonym selected from a London phone book and was sent to Taiwan to join Western Enterprises, a front organization that aimed to subvert Mao’s communist government in China. “The whole operation was a waste of time,” Dr. Coe said. Within a few years he was back at Harvard, studying for his doctorate.

In a phone interview, his former Yale colleague Mary Miller recalled that Dr. Coe “brought to the table from the very beginning a kind of fearlessness about trying new techniques and looking for new ways to solve problems.” He used a magnetometer to identify new monuments in San Lorenzo and championed an emerging approach known as ecological archaeology, studying the ways in which ancient peoples related to their environment.

He also risked his career in the 1960s to back the findings of Soviet linguist Yuri Knorozov, who argued — correctly — that the Maya writing system had a phonetic component. (Dr. Coe’s wife, the daughter of noted Ukrainian-American geneticist Theodosius Dobzhansky, translated many of Knorozov’s writings from Russian into English.)

In the face of opposition from preeminent Maya scholar J. Eric S. Thompson, Dr. Coe threw his support to Knorozov and co-wrote a 1968 article in which he translated the glyph for cage, showing how it contained individual syllables.

“It was a crystal-clear example that opened up how patterns could be studied to crack the code,” said Miller, a Mesoamerican art historian and director of the Getty Research Institute.

Dr. Coe was also closely identified with the Grolier Codex, which was said to have been found in a cave near Tortuguero, Mexico, before being acquired by a collector and displayed at a 1971 art exhibition organized by the Grolier Club in Manhattan.

Scholars questioned its authenticity, with one declaring that its contents — almanacs of Venus — were so confusing as to “make any Maya priest tear his long hair.” In an interview with the New York Times, Dr. Coe acknowledged that the document was “a real hot potato” but proclaimed that he would “stake my professional reputation on it.”

Its survival, he added, was “nothing less than a miracle.” Three other Maya books were known to have survived through the centuries, while countless texts had been destroyed by conquistadors and Catholic priests.

In 2016, a team of Mayanists including Dr. Coe conducted an analysis that supported the Grolier Codex’s authenticity. Two years later, researchers from Mexico’s National Institute of Anthropology and History reached the same conclusion — triggering a celebration that Miller described as vindication for Dr. Coe and, in a sense, the ancient Maya.

“Some of their last words,” she said, “would now be recognized and heard.”

Michael Douglas Coe was born in Manhattan on May 14, 1929. He grew up in Oyster Bay, N.Y., on a 400-acre family estate known as Planting Fields, now a state park.

Dr. Coe studied at St. Paul’s preparatory school in Concord, N.H., before entering Harvard. Working in the anthropology lab one day, he found himself alongside a Radcliffe student, Sophie Dobzhansky, measuring the cranial capacity of skulls by filling them with mustard seeds. They married in 1955.

Dr. Coe received a bachelor’s degree in 1950 and a doctorate in 1959. For a time, he worked in the field alongside his older brother, archaeologist William R. Coe, who helped dig the Maya city of Tikal out of the Guatemalan jungle.

They suffered a falling-out in the early 1960s and “never had anything else to do with each other,” Andrew Coe said. The brothers rarely spoke about each other, although one colleague recalled in a tribute that William sometimes discussed an incident in which Dr. Coe “left him in a deep excavation trench” during a dig in Belize. (William died in 2009.)

Dr. Coe joined the Yale faculty in 1960. He later chaired the anthropology department and was a curator at the school’s Peabody Museum of Natural History, in addition to serving as an adviser to Dumbarton Oaks, a Washington research institute affiliated with Harvard.

Survivors include five children and six grandchildren.

Dr. Coe’s many areas of expertise included the collapse of civilizations, and he sometimes noted that most lasted about 600 years — roughly the length of time since Western civilization flowered during the Renaissance. Environmental destruction and burgeoning population growth helped fell the Maya, he told the Guardian in 2008, and remained serious concerns across the planet.

“The difference is we have a choice whether to let things get worse or fix them,” he said. “That’s what science is about. But it takes will on the part of those who govern and those who are being governed. To tell you the truth, I don’t know if we have that.”

Correction: An earlier version of this obituary incorrectly reported that geneticist Theodosius Dobzhansky was born in the Soviet Union. He was born in what was then imperial Russia, now part of Ukraine. The story has been updated.