Several metazoan mitochondrial-trn genes (specifying tRNA) exhibit nucleotide triplets at specific and conserved positions corresponding to stop codons (TAG/TAA) and/or start codons (ATG/ATA). The products of these genes, which bear one or two types of these codons are called ss-tRNAs (for stop/start). In this article, several examples of ss-trn genes bearing start or stop codons in metazoans (protostomes and deuterostomes) strongly suggest that these codons are functional. Moreover, the ss-trn genes found in apicoplast genomes likely have a mitochondrial origin, but the TAR and ATR triplets (R for purines) found in their sequences seem to play only a structural role. Future investigations should attempt to clarify the mechanisms of the transcription and maturation of ss-trn genes with their overlapping protein genes and the possible regulatory roles of stop and start codons found in trn sequences.