Domestication has fascinated researchers starting with Charles Darwin who was the first to observe that domestication-related traits are similar across a variety of taxonomically distant domesticated species yet are very different for taxonomically close wild species. The genetic basis of domestication remains to be understood and there are at least three different hypotheses trying to explain the genetic mechanisms underlying domestication phenomenon. This commentary briefly reviews these hypotheses and the existing compelling evidence that mobile genetic elements contribute to the phenomenon of domestication.