Despite conservation in the arrangement of protein-coding and ribosomal RNA genes, the tRNA genes provide some surprising evolutionary insights. Most notably, we have discovered multiple heteroplasmic sites in tRNA genes that are also common to both species (Table 1, Table 2, Figure 2). Although one of these sites was previously known (Marcadé et al. 2007; Doublet et al. 2008), two are novel. The fact that all three of these shared heteroplasmies alter anticodon sequences, allowing these loci to function as dual tRNA genes, seems unlikely to be a chance occurrence. Although it is unclear exactly how long ago T. rathkei and C. convexus diverged, they are classified in different families, and the relatively low sequence identity of their mitochondrial genomes suggests they shared a common ancestor at least millions of years ago. Strong selection therefore seems likely to have maintained the crucial dual function of these genes for a very long time, and the atypical organization of the mitochondrial genome probably facilitates the evolution of such stable heteroplasmic sites. Conversely, selection to maintain the heteroplasmic sites probably also maintains the unusual linear/circular architecture of these mitochondrial genomes.