Formed in 2003 by Toby Driver after the break-up of Maudlin of the Well, they released their debut album Choirs of the Eye on John Zorn's Tzadik Records that same year.

Up until 2011, the lineup was constantly shifting, and Kayo Dot's sound consistently changed over the years, featuring a wide variety of instrumentation including guitar, drums, bass, violin, saxophone, vibraphone, synthesizers, clarinets and flutes.

Over the years, in addition to the rotating lineup and constantly changing sounds, Kayo Dot has been signed to a number of different record labels, Tzadik, Robotic Empire, Hydra Head, Driver's self-release imprint, Ice Level Music, The Flenser, and Prophecy Productions.

As of 2021, Kayo Dot has released ten studio albums, one EP and one split: Choirs of the Eye in 2003, Dowsing Anemone with Copper Tongue as well as Kayo Dot/Bloody Panda split in 2006, Blue Lambency Downward, Coyote in 2010, an EP titled Stained Glass in 2011, Gamma Knife in 2012 and a double-album Hubardo in 2013.

After reading online forums in which fans of Opeth and MOTW bickered over compositional styles, Driver decided to make a "through-composed metal album ... one without riffs or arbitrarily repeating parts.

Kayo Dot then signed to Robotic Empire Records and released its second album, Dowsing Anemone with Copper Tongue in January 2006.

[10] Despite retaining only two members (Driver and long time collaborator Mia Matsumiya), the band started work on a new album in late 2007.

[11] Driver and Matsumiya used several session musicians on this recording, including Skerik on saxophone and vibraphone, Hans Teuber on clarinet, and Charlie Zeleny on drums.

[14] After the poor critical reception and fan response to Blue Lambency Downward, Driver began working on a new long-form composition with Yuko Sueta, a NYC-based writer, filmmaker, and video artist.

[15] The album featured a rotating lineup of Driver on bass and vocals, Terran Olson on keyboards, David Bodie on drums, Mia Matsumiya on violin, Tim Byrnes on trumpet, and Daniel Means on woodwinds.

The remaining lyrics appear in the liner notes, some of which were later used in Jason Byron's book, "The Sword of Satan" which was included with the LP release of Hubardo in 2013.

Kayo Dot was left without financial support from a label and decided to stay independent, so the band recorded the album Gamma Knife live at a concert in Brooklyn, New York on October 5, 2011.

[18] The album was different in that it was recorded with a budget of zero dollars via six channels of microphones into a laptop helmed by a friend of the band, composer Jeremiah Cymerman.

[20] Gamma Knife was received critically better than the past few albums, as SputnikMusic gave it a 3.5/5 and said "for the first time in years, Kayo Dot feels musically relevant.

It was digitally released on September 10, 2013, to widespread acclaim, and received good reviews from multiple sources [23] Through crowd-funding, Kayo Dot self-released a triple LP that sold out immediately, containing a 40-page book/poem by former Maudlin of the Well guest vocalist Jason Byron entitled "The Sword of Satan."

[28] In September 2018, Kayo Dot signed with the German record label Prophecy Productions, also announcing work had begun on a new album.

[2] A video was created for the first single, "Void in Virgo (The Nature of Sacrifice)," by musician, writer, and filmmaker Nick Jack Hudson.

The label on their debut reads, "Kayo Dot powerfully integrates elements of modern classical composition with layers of guitars and vocals more common to rock and metal."

Loud walls of guitars and quiet interludes are equally common, which has led to their music being labeled post-metal, post-rock, progressive rock and avant-garde.

Toby Driver has said that his influences in Kayo Dot include artists such as The Cure, Scott Walker, Emperor, Ulver, John Zorn, Gorguts, Björk, and Susumu Hirasawa.