Otto Kandler (born 23 October 1920 in Deggendorf, Bavaria) is a German Botanist and Microbiologist.
With Carl Woese Kandler proposed the change from the preceding view of living organisms as a Two-empire system of Prokaryotes and Eukaryotes to the Three-domain system of the domains Eukaryota, Bacteria and Archaea. While bacteria and archaea appear to be similar in form and structure, Woese, Kandler and Wheelis demonstrated that they were genetically very dissimilar. They demonstrated this through analysis of Ribosomal RNA.
Kandler taught and conducted research at Ludwig Maximilian University of Munich from 1968 to 1986. Kandler became a member of the Bavarian Academy of Sciences and Humanities in 1983.
The methanogen Methanopyrus kandleri (Kurr, 1991) was named in honor of Kandler.