The prevalence and distribution of pMEA-like elements in the genus Amycolatopsis was studied. For this purpose, a set of 95 recently isolated Amycolatopsis strains and 16 Amycolatopsis type strains were examined for the presence of two unique pMEA-sequences (repAM and traJ), encoding proteins essential for replication and conjugative transfer. Homologues of repAM and traJ were found in 10 and 26 of 111 investigated strains, respectively, a result which shows that pMEA-like sequences, though not very abundant, can be found in several Amycolatopsis strains. Phylogenetic analysis of the deduced RepAM and TraJ protein sequences revealed clustering with the protein sequences of either pMEA300 or pMEA100. Furthermore, two geographically different populations of pMEA-like elements were distinguished, one originating in Europe and the other in Australia and Asia. Linkage between the distribution of repAM and traJ and the chromosomal identifier, the 16S rRNA gene, indicated that these elements coevolved with their hosts, suggesting that they evolved in an integrated form rather than by horizontal gene transfer of the free replicating form.