RNA silencing includes a diverse family of processes featuring small RNAs (sRNAs) produced by Dicer-mediated cleavage of a double stranded or based paired precursor. These sRNAs are versatile regulatory molecules acting within or between cells and it is likely that they are derived from a primitive defense system against viruses. Over evolutionary time, however, the functions of this process have diversified. One variation in tomato retains the ancestral function in that it provides defense against endogenous (pararetro)viruses. Additionally it also influences gene expression in interspecific hybrids. Other variations on the ancestral process influence non-Mendelian inheritance resulting in paramutation-like effects and provide feedback regulation of the innate immune system. These various findings illustrate how parasites and the defense systems against provide substrates for evolutionary diversification that benefit the host organism.