Despite the increasing credence accorded the concept, the ecology of extrachromosomal elements is still poorly documented, theories concerning their phylogeny and interrelationships are speculative, and the terminology applied to such agents remains confused. In many instances, extrachromosomal elements are regarded as bizarre curiosities that are something of an epiphenomenon in general evolutionary biology. The present review attempts to construct a balanced theory of evolution in which proper emphasis is given to possible roles for plasmids and viruses in the processes of growth, adaptation, and speciation.