Cytogenetics was born of the confluence of two so-far independent fields: cytological studies and breeding studies, which merged through the identification of genes with chromosomes. In this paper I argue that genes were introduced as functional entities. Functional explanations are presented here as a subclass of inferences to the best explanation and I argue that abductive arguments do not offer conclusive proof for the existence of the entities postulated through them. However, functional explanations usually follow a scheme laid out by Fodor (1968): there is a first phase where hypothetical entities are postulated and individuated through their effects; there is a second phase where the physical structures responsible for these effects are sought. I analyze the development of both phases in the construction of the chromosome theory of Mendelian inheritance. I will argue that first-phase theories are important to set conditions of identification for the functions played by a certain structure in a given containing system.