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Background  The mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Although the loss of genes is rare in Sarcoptiformes mite mitogenomes, two of the six previously reported oribatid mites (Acariforms: Sarcoptiformes) are reported to have lost parts of their tRNA genes. To confirm whether the tRNA genes were indeed lost and whether the loss is universal, we re-annotated the available oribatid mite sequences and sequenced the mitogenome of  Oribatula sakamorii .    Methods  The mitogenome of  O .  sakamorii  was sequenced using an Illumina HiSeq sequencer. The mt tRNA gene was annotated using multi-software combined with a manual annotation approach. Phylogenetic analyses were performed using the maximum likelihood and Bayesian inference methods with concatenated nucleotide and amino acid sequences.    Results  The mitogenomes of  O .  sakamorii  contained 37 genes, including 22 tRNA genes. We identified all mt tRNA genes that were reported as “lost” in  Steganacarus magnus  and  Paraleius leontonychus  and revealed certain atypical tRNA annotation errors in oribatid mite sequences. Oribatid mite mitogenomes are characterized by low rates of genetic rearrangement, with six or seven gene blocks conserved between the mitogenome of all species and that of ancestral arthropods. Considering the relative order of the major genes (protein-coding genes and rRNAs), only one or two genes were rearranged with respect to their positions in the ancestral genome. We explored the phylogenetic relationships among the available oribatid mites, and the results confirmed the systematic position of  Hermannia  in the Crotonioidea superfamily. This was also supported by the synapomorphic gene-derived boundaries.    Conclusions  The tRNA “lost” phenomenon is not universal in oribatid mites. Rather, highly atypical secondary structure of the inferred mt tRNA genes made them unidentifiable using a single type of tRNA search program. The use of multi-software combined with a manual annotation approach can improve the accuracy of tRNA gene annotation. In addition, we identified the precise systematic position of  Hermannia  and validated that Astigmata is nested in Oribatida.    Graphic AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04719-0.

Mitochondrial analysis of oribatid mites provides insights into their atypical tRNA annotation, genome rearrangement and evolution