This paper studies the reception of Ernst Haeckel's (1834-1919) ideas in Greece during the late 19th. Ernst Haeckel was a very controversial figure associated with the group of German materialists, such as Bόchner, Moleschsott and Vogt. Haeckel was a proponent of physicalism (physiocratic materialism) and a strong advocate of the Darwinian theory of evolution. Today is widely known due to his work on the foundations of the science of Ecology. Although a number of different issues arise from the discussion of Haeckel's ideas, this work focuses on the materialism - idealism controversy and the axes on which the controversy is centered. This controversy is still relevant in our days with certain aspects of the science - religion dipole influencing not only scientific research but science education as well.