The predominant current-day meaning of genotype is the DNA passed to the organism by its parents at the organism’s conception. The phenotype is the physical and behavioral characteristics of the organism, for example, size and shape, metabolic activities, and patterns of movement. To examine the relationship between the genotype and the phenotype is to be drawn into investigations that include: identification—what can be inferred about a genotype from a phenotype; breeding and evolution—the connection between a phenotype’s contribution to survival and reproductive success and changes in the frequency of genotypes in a population over time; development—the role of the genotype in the pathways through which the phenotype develops over an organism’s lifespan; and barriers—how well the genotype is shielded from the processes and outcomes of development. When philosophers contribute to current discussion of these questions, it is generally not the distinction between genotype and phenotype that is of concern. The genotype-phenotype distinction can, nevertheless, be seen as interesting philosophically once it is recalled that the meanings given to the key terms were quite different when Johannsen (1911) introduced them to English-language readers. Teasing out conceptual and methodological problems raised or implied in that article provides a basis for reviewing the subsequent shifts in meaning of the terms and various attempts to address—or suppress—those problems. To examine these issues is to explore the implications of two foundational developments of modern biology—the theories of evolution by natural selection and the genetic basis of heredity—having been built from the language, arguments, evidence, and practices of controlled breeding in agriculture and the laboratory.