Markoff was born in Oakland, California and grew up in Palo Alto, California. He graduated from Bryn Mawr College, Bryn Mawr Pennsylvania, in 1970 and received a Master's degree from Mills College in 1976.

After leaving graduate school, he returned to California where he began writing for Pacific News Service, an alternative news syndicate based in San Francisco. He freelanced for a number of publications including the Nation, Mother Jones and Saturday Review. In 1981 he became part of the original staff of the computer industry weekly InfoWorld. In 1984 he became an editor at Byte Magazine and in 1985 he left to become a reporter in the business section of the San Francisco Examiner, where he wrote about Silicon Valley.

In 1988 he moved to New York to write for the business section of the New York Times. In November 1988 he reported that Robert Tappan Morris, son of National Security Agency cryptographer Robert Morris, was the author of what would become known as the Internet worm.

In December 1993 he wrote an early article about the World Wide Web, referring to it as a "map to the buried treasures of the Information Age."

Markoff and Kevin Mitnick

On July 4, 1994 he wrote an article about Kevin Mitnick, who was then a fugitive on the run from a number of law enforcement agencies. He wrote several more pieces detailing Mitnick's capture. Markoff also co-wrote, with Tsutomu Shimomura, the book Takedown about the chase. The book later became a film that was released direct to video in the United States. Markoff's writing about Mitnick was the subject of criticism by Mitnick supporters and unaffiliated parties who maintained that Markoff's accounts exaggerated or even invented Mitnick's activities and successes. Markoff stood by his reporting in several responses.

The film went far further, with Markoff himself stating to the San Francisco Chronicle in 2000, "I thought it was a fundamentally dishonest movie." (Mitnick stated a number of times that he settled a lawsuit with distributors Miramax over the film, but details were confidential; Miramax has apparently never publicly confirmed that.)

Markoff was also accused by Jonathan Littman of journalistic impropriety and of over-hyping Mitnick's actual crimes. Littman published a more sympathetic account of Mitnick's time as a fugitive in his own book on the incident, The Fugitive Game. Further controversy came over the release of the movie Takedown, with Littman alleging that portions of the film were taken from his book The Fugitive Game without permission.

Post-Mitnick

After Mitnick, Markoff continued to write about technology, focusing at times on wireless networking, writing early stories about non-line-of-sight broadband wireless, phased-array antennas, and multiple-in, multiple-out (MIMO) antenna systems to enhance Wi-Fi. He covered Jim Gillogly's 1999 break of the first three sections of the CIA's Kryptos cipher [1], and writes regularly about semiconductors and supercomputers as well. He wrote the first two articles describing Admiral John Poindexter's return to government and the creation of the Total Information Awareness project. Since 2009 he moved from the Business/Tech section of the New York Times to the Science section.