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Controversy Over Relation to Nazism
Some historians have seen Haeckel's social Darwinism as a forerunner to National Socialist ideology. Others have denied the relationship all together.

The evidence is in some respects ambiguous. On the one hand, Haeckel was an advocate of scientific racism. He held that evolutionary biology had definitively proven that races were unequal in intelligence and ability, and that their lives were also of unequal value. As a result of the "struggle for existence," it followed that the "lower" races would eventually be exterminated. He was also a social Darwinist who believed that "survival of the fittest" was a natural law, and that struggle led to improvement of the race. As an advocate of eugenics, he also believed that about 200,000 mentally-ill and congenitally-ill should be murdered by a medical control board. (This idea was later put into practice by the Third Reich, as part of the Aktion T4 program.) Haeckel also believed that Germany should be governed by an authoritarian political system, and that inequalities both within and between societies were an inevitable product of evolutionary law. Haeckel was also an extreme German nationalist who believed strongly in the superiority of German culture. . On the other hand, Haeckel was not an anti-Semite. In the racial hierarchies he constructed, Jews tended to appear closer to the top than the bottom (as in National Socialist racial thought.). He was also a pacifist until the First World War, when he wrote propaganda in favor of the war. The principal arguments of historians who deny a meaningful connection between Haeckel and National Socialism is that Haeckel's ideas were very common at the time, that National Socialists were much more strongly influenced by other thinkers, and that Haeckel is properly classified as a 19th century German liberal, rather than a fore-runner to 20th century National Socialism.

Some Nazis held him in high regard. S.S. captain and biologist Heinz Brücher wrote a biography of Haeckel in 1936, in which he praised Haeckel as a "pioneer in biological state thinking." This opinion was also shared by the scholarly journal, Der Biologie, which celebrated Haeckel's 100th birthday, in 1934, with several essays acclaiming him as a pioneering thinker of National Socialism.

Other Nazis kept their distance from Haeckel. Nazi Propaganda guidelines issued in 1935 listed books which popularized Darwin and evolution on an "expunged list." Haeckel was included by name as a forbidden author. Gunther Hecht, a member of the Nazi Department of Race Politics, also issued a memorandum rejecting Haeckel as a forerunner of National Socialism. Kurt Hildebrandt, a Nazi political philosopher, also rejected Haeckel. . Historian Robert Richards argues that National Socialists at first embraced Haeckel, but quickly rejected him after they realized that Haeckel's ideas were incompatible with their own. .