Two complete mitochondrial genomes (mtDNAs) of chaetognaths, Spadella cephaloptera and Paraspadella gotoi, have been recently published. These genomes are highly unusual. They are the smallest metazoan mtDNAs so far known; atp6 and atp8 genes are missing; lastly, our reanalysis has evidenced that, contrarily to what has been previously published for one sequence, both contain a unique transfer RNA (tRNA(Met)) evidencing that both have the same gene content. Indeed, even if the gene order seems very different, two gene blocks are conserved. In addition, comparison of gene arrangement suggests phylogenetical relationships between chaetognaths and some lophotrochozoa like annelids and molluscs.