Here, we further explore the evolution of mitochondrial genomes in terrestrial isopods with complete mitochondrial genome sequences for two additional species, Trachelipus rathkei and Cylisticus convexus. The relative order of protein-coding and rRNA genes is conserved, whereas the arrangement of tRNA genes is more variable. Strikingly, we found two additional heteroplasmic sites that also alter anticodon sequences in tRNA genes and are both conserved across these two species. We discuss the implications of these findings for the evolution of tRNA genes and mitochondrial genome architecture in general.