Jonathan Bayliss was born on September 7, 1926, in Arlington, Massachusetts. His parents, Henry and Lois Henderson Balos, divorced in 1932, after which Lois — adopting the name Bayliss — raised her three children alone. She moved the family frequently during the Great Depression. Jonathan and his younger sister and brother attended public schools in Cambridge, Massachusetts, and Arlington, Vermont. Later Jonathan won a scholarship to the Newton School, South Windham, Vermont, where his jobs included felling trees for lumber and milking cows.

Bayliss enrolled at Harvard in 1943, served in the U.S. Navy toward the end of World War II, and finished his A.B. at the University of California at Berkeley in 1949. Bayliss and Doris Sturtevant married in 1948. Two daughters were born in Oakland, California. The family moved East in 1953, living first in Newton Corner, Massachusetts, and then in Gloucester starting in 1956. A son was born in Gloucester in 1960. The marriage ended in 1966.

While writing his Gilgamesh plays and the GLOUCESTERMAN novels, the work of a lifetime, Bayliss earned a livelihood in positions involved with sales analysis, accounting controls, and management, beginning in 1950 at a Berkeley bookstore.

In the 1960s, as controller at Gorton’s of Gloucester, the frozen-fish processor based in Gloucester, Massachusetts, he was a pioneer in developing integrated business applications for the IBM System 360. Working closely with the architect Eduardo Catalano, he also supervised the design and construction of a new Gorton’s headquarters building. After leaving Gorton’s in 1972, Bayliss devoted the next five years to full-time writing, with the help of a literary grant from the Massachusetts Arts and Humanities Foundation. Later, after the grant funding ran out, he worked for the City of Gloucester as an executive aide to the mayor and as city treasurer. In 1985 he resumed full-time writing.

Bayliss was putting the finishing touches on his final novel, Gloucestermas, when he died in 2009 at Addison Gilbert Hospital, Gloucester, at the age of 82. Cause of death was a cerebral hemorrhage. Bayliss's ashes are buried in Mount Auburn Cemetery, Cambridge, in his mother's family's plot.

Bayliss’s manuscripts and papers are in the collection of Houghton Library at Harvard University.

Five of Bayliss's literary friends were interviewed on videotape in 2009 after his death; portions of those interviews, which provide glimpses into Bayliss's interests and his work, are now available to watch here. Other links to Bayliss materials are available at gloucesterman.org.