His death was announced by the University of Illinois, where Dr. Woese (pronounced woes) joined the faculty in 1964 and spent his entire academic career.

In 1977, Dr. Woese and colleagues at the university startled the scientific world by announcing the discovery of what would be called archaea, a category of single-cell microbes genetically distinct from the two groups previously believed to comprise living organisms: prokaryotes, which include bacteria, and eukaryotes, which include plants and animals.

While other evolutionary biologists had long studied physical traits of species to determine their relationships, Dr. Woese spent years laboriously comparing the genetic sequences of protein-building structures in cells, known as ribosomes and ribosomal DNA. In the process, he established that archaea, which had previously been thought to be within the prokaryote group, had in fact evolved separately from a universal ancestor shared by all three groups.

"He put on the table a metric for determining evolutionary relatedness," said Norman R. Pace, a microbiologist and biochemist at the University of Colorado, Boulder. "His results were the first to prove that all life on earth was related."

Archaea, which are relatively simple genetically, were initially believed to exist only in extreme environments like undersea volcanic vents and hot springs. In the years since Dr. Woese's initial research, they have been found in many places, including in plankton and in the human body.

As his work became commonly accepted, Dr. Woese urged other scientists to pursue the territory further. He argued that understanding the evolution of microbes was central to understanding evolutionary biology.

"It's clear to me that if you wiped all multicellular life-forms off the face of the earth, microbial life might shift a tiny bit," Dr. Woese said in an interview with The New York Times in 1996. "If microbial life were to disappear, that would be it — instant death for the planet."

He noted that microbes, although invisible, make up far more of the living protoplasm on earth than all humans, animals and plants combined. Yet there had been little study of them.

"Imagine walking out in the countryside and not being able to tell a snake from a cow from a mouse from a blade of grass," he said. "That's been the level of our ignorance."

Carl Richard Woese was born July 15, 1928, in Syracuse. He earned bachelor's degrees in math and physics from Amherst College in 1950 and a Ph.D. in biophysics at Yale in 1953. He studied medicine for two years at the University of Rochester, spent five years as a researcher in biophysics at Yale and worked as a biophysicist at the General Electric Research Laboratory in Schenectady, N.Y., before joining the faculty of the University of Illinois in 1964.

Dr. Woese received many honors and awards, including a MacArthur Foundation "Genius" grant in 1984, the National Medal of Science in 2000 and the Crafoord Prize in Biosciences from the Royal Swedish Academy of Sciences in 2003, which recognized his "discovery of a third domain of life."

His survivors include his wife, Gabriella; a sister, Donna Daniels; a daughter, Gabriella, and a son, Robert.

In a statement released by the University of Illinois, Nigel Goldenfeld, a longtime colleague, noted that Dr. Woese had entered the field as an "outsider" whose methods were not traditional.

"He turned a field that was primarily subjective into an experimental science," Dr. Goldenfeld said, "with wide-ranging and practical implications for microbiology, ecology and even medicine that are still being worked out."