Theodor Boveri's major intellectual contribution was his focus on the causality of nuclear chromosomal determinants for embryological development. His initial experimental attempt to demonstrate that the character of the developing embryo is determined by nuclear rather than cytoplasmic factors was launched in 1889. The experimental design was to fertilize enucleate sea urchin eggs with sperm of another species that produces a distinguishably different embryonic morphology. Boveri's "hybrid merogone" experiment provided what he initially thought was empirical evidence for the nuclear control of development. However, for subtle reasons, the data were not interpretable and the experiment was repeated and contested. At the end of his life, Boveri was finally able to explain the technical difficulties that had beset the original experiment. However, by 1902 Boveri had carried out his famous polyspermy experiments, which provided decisive evidence for the role of nuclear chromosomal determinants in embryogenesis. Here we present the history of the hybrid merogone experiment as an important case of conceptual reasoning paired with (often difficult) experimental approaches. We then trace the further history of the merogone and normal species hybrid approaches that this experiment had set in train, and review their results from the standpoint of current insights. The history of Boveri's hybrid merogone experiment suggests important lessons about the interplay between what we call "models", the specific intellectual statements we conceive about how biology works, and the sometimes difficult task of generating experimental proof for these concepts.