Publisher Summary This chapter describes the mithochondrial genome of ciliates, with emphasis on Paramecium and Tetrahymena . Both Paramecium and Tetrahymena have linear genomes with unique replicative pathways. The mitochondrial genome of Paramecium aurelia is a linear duplex. Replication is initiated at a unique end and preceded undirectionally, resulting in a head-to-head dimer intermediate. The most unusual feature of this mechanistic scheme is the apparent linkage of the complementary strands at the initiation end of the molecule. By taking advantage of the availability of dimer molecules, the double-stranded initiation region is cloned and the entire region from five different species is sequenced. For all species, this dimer initiation region contains a series of A T-rich repeats, specific for each species. On the other hand, the mitochondrial genome of Tetrahymena pyriformis provides an interesting complement to that from P. aurelia . The DNAs of all strains differ in size and the size variation is entirely dependent on the size of a duplication–inversion present at both ends. The duplication–inversion has two components: a duplicate large subunit ribosomal RNA gene and a set of repeated sequences.