The recent adoption of whole plasmid genome sequencing as a routine analytical technique has provided the basis for cataloging the historical events through which plasmids are assembled from the available families of modular plasmid components. Horizontal gene transfer mediated by plasmids plays an important role in the adaptation of bacteria to the presence of specific metabolizable compounds, including man-made chemicals, in the surrounding environment. Bacterial plasmid genome sequence comparisons indicate that plasmids have complex genetic histories resulting from transposition, homologous recombination, and illegitimate recombinational events. Evidence from IncP plasmid genome sequences indicates that cryptic plasmid backbones acquire diverse catabolic pathways through gene capture and horizontal gene transfer.