Significance The notion of genetic dominance was first introduced by Gregor Mendel and is defined as the relationship between alleles of the same gene in which one allele (dominant) masks the phenotypic contribution of a second allele (recessive). The effect of genetic dominance on bacterial evolution has generally been neglected because most bacteria of human interest carry a single copy of their chromosome. However, bacteria also carry mobile genetic elements (MGE), which produce local islands of polyploidy. This polyploidy arises both from the multicopy nature of MGE and from the allelic redundancy between MGE and chromosomal genes. Here we show that genetic dominance dictates both the evolution and successful spread of genes encoded on MGE, shaping horizontal gene transfer in bacteria.