Ernst Märzendorfer (26 May 1921 – 16 September 2009) was an Austrian conductor.

Märzendorfer was born in Oberndorf bei Salzburg. He studied with Clemens Krauss at the Mozarteum in Salzburg, and was appointed as first conductor of the Graz Opera in 1945. He conducted at the Teatro Colón in Buenos Aires in the early 1950s. In 1954 he became a guest conductor at the Salzburg Festival. From 1953 to 1958, he was the principal conductor of the Mozarteum Orchestra of Salzburg, and led several tours with the orchestra, including a highly acclaimed American tour.

He was appointed musical director of the Salzburg Festival in Hellbrunn in 1976, where his highlights included twenty stage works by Jacques Offenbach. He was permanent conductor at the Vienna State Opera in from 1961, and often appeared at the Berlin State Opera. In 1979 he revived Franz Schmidt's opera Fredigundis.

He died aged 88 in Vienna.