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After their discovery in the first decades of the 20th century, pseudo-alleles generated much interest among geneticists, because they apparently violated the conception of the genome as a collection of independent genes, a view elaborated by Thomas Morgan’s group. This article focuses on two issues: the way the phenomenon of pseudoallelism suggests that the genome is more than a simple addition of independent genes, and the connection established between the formation of pseudoalleles during evolution and their functional roles. The article discusses the first explanations for the origin of pseudoalleles elaborated in the mid-1930s, the metabolic/developmental sequential model proposed by Ed Lewis in the 1950s, the disappointments encountered with the T-complex in the 1970s, and the fading of the previous models after the molecular characterization of the pseudoallelic gene complexes in the 1980s. Genomes are more than collections of genes, but their structures are the result of a complex evolutionary history that leaves no place for simplistic models.