This article provides an initial analysis, from a historical standpoint, of the problematic nature of conceptualizations of the notion of gene in molecular genetics. The starting point is an historical outline of the relation between classical genetics and molecular genetics; it is indicated how the conceptual baggage of classical genetics influenced the development of the concepts of gene used later in molecular biology. I also reveal two problems of genes in the philosophy of science, i.e., skepticism concerning genes and the concept of nominal gene. I conclude that concept of gene functioning within the framework of molecular genetics should be considered from the point of view of experimentalism and pragmatism. It seems that the concept of gene on the molecular level should be conceptualized—in order to remain functional—as broadly as possible and in relation to genetic material.