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With Carl Gegenbaur and Ernst Haeckel, inspired by Darwin and the cell theory, comparative anatomy and embryology became established and flourished in Jena. This tradition was continued and developed further with new ideas and methods devised by some of Haeckel's students. This first period of innovative work in evolutionary morphology was followed by periods of crisis and even a disintegration of the discipline in the early twentieth century. This stagnation was caused by a lack of interest among morphologists in Mendelian genetics, and uncertainty about the mechanisms of evolution. Idealistic morphology was still influental in Germany, which prevented a full appreciation of the importance of Darwin's theory of natural selection for comparative morphology. Evolutionary morphology and embryology failed to contribute significantly to the modern synthesis of evolutionary biology, thereby probably delaying the integration of developmental biology into modern evolutionary biology. However, Haeckel's student Oscar Hertwig, as well as Victor Franz and Alexej N. Sewertzoff from a younger generation, all tried to forge their own synthetic approaches in which (inspired by Haeckel's work) embryology played an important role. Important for all three researchers were attempts to refine, and sometimes redefine, the biogenetic law, and to find new scientific explanations for it (and for the many exceptions to it). Their research was later more or less forgotten, and had little influence on the architects of the modern synthesis. As the relationship between evolutionary and developmental biology is now again rising in importance in the form of “Evo-Devo”, we would like to draw attention to how this earlier research tradition grappled with similar questions to those now on the agenda, albeit from sometimes quite different perspectives.