CRISPR/Cas and CRISPR/Cmr immune machineries of archaea and bacteria provide an adaptive and effective defence mechanism directed specifically against viruses and plasmids. Present data suggest that both CRISPR/Cas and Cmr modules can behave like integral genetic elements. They tend to be located in the more variable regions of chromosomes and are displaced by genome shuffling mechanisms including transposition. CRISPR loci may be broken up and dispersed in chromosomes by transposons with the potential for creating genetic novelty. Both CRISPR/Cas and Cmr modules appear to exchange readily between closely related organisms where they may be subjected to strong selective pressure. It is likely that this process occurs primarily via conjugative plasmids or chromosomal conjugation. It is inferred that interdomain transfer between archaea and bacteria has occurred, albeit very rarely, despite the significant barriers imposed by their differing conjugative, transcriptional and translational mechanisms. There are parallels between the CRISPR crRNAs and eukaryal siRNAs, most notably to germ cell piRNAs which are directed, with the help of effector proteins, to silence or destroy transposons. No homologous proteins are identifiable at a sequence level between eukaryal siRNA proteins and those of archaeal or bacterial CRISPR/Cas and Cmr modules.