Here we report on a recently discovered student script of a lecture on paleontology given by Ernst Haeckel (1834–1919). The script dates to the summer semester of 1866, comprises 63 pages, and provides an overview of fossil invertebrate and mainly fossil vertebrate taxonomy and anatomy. It can be assumed that Russian student Nikolai Nikolajevitch Miklucho-Maclay (1846–1888), who later became a famous ethnologist, did not follow up on the lecture, but took the content directly from the lecture and from the blackboard in his notes. Hence, the drawings by Miklucho allow direct insight into Haeckel’s visualization of paleontology in the 1860s. We place the transcript in the historical context of understanding paleontology in the second half of the 19thcentury and address the break between zoology and embryology on the one hand and paleontology on the other, which is typical for Germany, partly persisting to this date. For that, we illustrate Haeckel’s integration of paleontology as part of a holistic triad, with fossil research gradually taking a back seat to zoology and embryology over the decades.