Abstract The evolutionary origin of turtles has long been debated, and recent studies continue to provide conflicting results. In some of the first trees of organisms ever drafted, Ernst Haeckel (1834–1919) placed turtles close to birds based on morphological arguments. He only later became convinced by novel embryological and paleontological discoveries that birds are rather placed within dinosaurs, far removed from turtles. We analyzed Haeckel’s major publications on vertebrate phylogeny, with a focus on turtles and birds, and discuss his arguments for alternative interpretations of land vertebrate phylogeny. Haeckel carefully took the most recent developments in biology and paleontology into account to create his trees of life. While using his concept of the trifold parallelism between embryology, paleontology, and comparative anatomy, he understood his phylogenies as “fluent working hypotheses” with branches and taxon names floating, depending on available scientific evidence. Although Haeckel's trees resemble modern trees in many regards, he often pursued hypotheses not supported by recent data. We conclude that he committed those because of his strict attempts to order taxa by morphological homogeneity while not taking convergences into account.