It was originally isolated from the deep sea, with various strains being isolated from sediment, a clam, and a crab.

[1] It is notable among the Kluyveromyces species as the only member unable to ferment glucose.

[1][2] In 1999, eleven strains of a previously unknown Kluyveromyces species were discovered in deep-sea samples from Suruga Bay and Sagami Bay off the coast of Honshu, Japan.

The samples originated from marine sediment, a Calyptogena clam, and an unknown crab species.

[1] At the time of discovery, K. nonfermentans was determined to be most closely related to Kluyveromyces aestuarii based on 18S rRNA gene sequences.