Most characterised metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analysed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three 'ORFane' regions (1063, 427, and 519 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known spionidae mitogenomes. By analysing the ORFane sequences, we found that they are under negative selection pressure, contain conservative regions, and harbour predicted transmembrane domains.The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. Together, this suggests that ORFanes encode functional proteins. We speculate that the ORFanes originated from the conventional mitochondrial protein-coding genes which were duplicated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae.