Prokaryotes are constantly being infected by large mobile genetic elements (MGEs) such as conjugative elements and temperate phages. The fitness of these elements is tightly linked with the evolutionary success of the host. This leads to selection against disruptive effects their integration might have on the organization and structure of the chromosome. Seamless genetic accommodation of the mobile elements also involves silencing infectious mechanisms and expressing functions adaptive to the host. Ironically, these characteristics favor the host ability to domesticate the mobile element. Recent data suggest that the domestication of mobile elements might be frequent. Importantly, it might affect the evolution of chromosome organization and drive the diversification of social traits.