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Background  Complete mitochondrial (mt) genomes and the gene rearrangements therein are increasingly used as molecular markers for investigating phylogenetic relationships, especially for elucidating deep splits. Contributing to the complete mt genomes of arthropods, especially Arachnida, available so far, we provide the first complete mt genome of a sarcoptiform mite species, the sexually reproducing oribatid mite  Steganacarus magnus  (Acari, Oribatida) which was determined by sequencing of long PCR products.    Results  The mt genome of  S. magnus  lacks 16 tRNAs, only those for leucine, histidine, proline, tryptophan, glutamine and serine are present. Within those tRNAs only tRNA-His and tRNA-Pro have kept their original position, the others are translocated. Furthermore, the mt genome of  S. magnus  consists of 13,818 bp and it is composed of 13 protein-coding genes and two genes for the ribosomal RNA subunits that are typically found in metazoan mt genomes. The gene order in  S. magnus  differs from the hypothetical ancestral chelicerate arrangement as conserved in  Limulus polyphemus : instead of  nad1-rrnL-rrnS -LNR- nad2  (tRNAs excluded)  S. magnus  is  nad2-rrnL-nad1-rrnS -LNR. Phylogenetic analyses of a concatenated amino acid dataset of all mt protein-coding genes of 28 arthropod species suggest a sister-group relationship of sarcoptiform and prostigmatid mites ( S. magnus  and  Leptotrombidium ).    Conclusion  The mt gene arrangement of  S. magnus  differs from the hypothetical ground plan of arthropods and from that of other mites further contributing to the variety of mt gene arrangements found in Arachnida. The unexpected lack of tRNAs is enigmatic, probably showing that the loss of mt genes is an ongoing evolutionary process. For solving phylogenetic relationships of oribatid mite lineages and their position within Acari further complete mt genomes are needed.

The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs