The platypus mitochondrial control region has been cloned and sequenced. Comparative analysis of this sequence with the published control region sequences of several other mammalian species has identified regions of sequence consensus that are conserved throughout the Mammalia. Regions predicted to form thermodynamically stable secondary structures in the platypus are also homologous to such putative structures in other species. In addition to these conserved structures, the platypus mitochondrial control region also contains a number of unusual features, including two regions of repetitive sequence, one of which gives rise to pronounced length variation between animals. Possible functions for the conserved structures and a mechanism for the generation of the control region length variation are proposed with respect to our current understanding of mitochondrial replication and transcription.