Haeckel was also known for his "biogenic theory", in which he suggested that the development of races paralleled the development of individuals. He advocated the idea that "primitive" races were in their infancies and needed the "supervision" and "protection" of more "mature" societies.

He extrapolated a new religion or philosophy called Monism from evolutionary science. In Monism, all economics, politics, and ethics are reduced to "applied biology." His writings and lectures on Monism provided scientific (or quasi-scientific) justifications for racism, nationalism and social Darwinism. It has even been argued that monism thus became the de facto religion of Nazi Germany. Other scholars disagree, arguing that Nazi ideology was not comfortable with evolutionary theory, which argues for a common descent of all human races.

Haeckel was a flamboyant figure whose was more popular with the public than with his scientific peers. He sometimes took great (and non-scientific) leaps from available evidence. For example, at the time that Darwin first published On the Origin of Species by Means of Natural Selection, no remains of human ancestors had yet been found. Haeckel postulated that evidence of human evolution would be found in the Dutch East Indies (now Indonesia), and described these theoretical remains in great detail. He even named the as-of-yet unfound species, Pithecanthropus alalus, and charged his students to go find it.

Remarkably, one of them did so — a young Dutchman named Eugene Dubois went to the East Indies and dug up the remains of Java Man, the first human ancestral remains ever found. (These remains originally carried Haeckel's Pithecanthropus label, though they were later reclassified as Homo erectus.)

Although Haeckel's ideas are important to the history of evolutionary theory, and he was a competent invertebrate anatomist most famous for his work on radiolaria, most of the speculative concepts that he championed are now seen as incorrect. For example, Haeckel described and named hypothetical ancestral microorganisms that have never been found. His concept of recapitulation called "strong recapitulation" has been disputed. Haeckel did not support Darwin's "survival of the fittest", rather believing in a Lamarckian inheritance of acquired characteristics.

Richard and Oskar Hertwig were some of Haeckel´s many important students.

Mount Haeckel is a 4090 m (13,418') summit in the Eastern Sierra Nevada, overlooking the Evolution Basin, named in honor of Ernst Haeckel as is the asteroid 12323 Häckel. Ernst Haeckel, much like Herbert Spencer, was always quotable, even when wrong. Although best known for the famous statement "ontogeny recapitulates phylogeny", he also coined many words commonly used by biologists today, such as phylum, phylogeny, and ecology. On the other hand, Haeckel also stated that "politics is applied biology", a quote used by Nazi propagandists. The Nazi party, rather unfortunately, used not only Haeckel's quotes, but also Haeckel's justifications for racism, nationalism and social Darwinism.

Although trained as a physician, Haeckel abandoned his practice in 1859 after reading Darwin's Origin of Species. Always suspicious of teleological and mystical explanation, Haeckel used the Origin as ammunition both to attack entrenched religious dogma and to build his own world view.

Hackel studied under Carl Gegenbauer in Jena for three years before becoming a professor of comparative anatomy in 1862. Between 1859 and 1866, he worked on many "invertebrate" groups, including radiolarians, poriferans (sponges) and annelids (segmented worms). He named nearly 150 new species of radiolarians during a trip to the Mediterranean. "Invertebrates" provided the fodder for most of his experimental work on development, leading to his "law of recapitulation". Haeckel was also a free-thinker who went beyond biology, dabbling in anthropology, psychology, and cosmology. Haeckel's speculative ideas and possible fudging of data, plus lack of empirical support for many of his ideas, tarnished his scientific credentials. However, he remained an immensely popular figure in Germany and was considered a hero by his countrymen.