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Background  Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in  Aleuroglyphus ovatus ,  Caloglyphus berlesei ,  Dermatophagoides farinae ,  D. pteronyssinus ,  Histiostoma blomquisti  and  Psoroptes cuniculi . Loss of 16 mt tRNA genes, however, was reported in  Steganacarus magnus ; loss of 2–3 tRNA genes was reported in  Tyrophagus longior ,  T. putrescentiae  and  Sarcoptes scabiei . Nevertheless, convincing evidence for mt gene loss is lacking in these mites.    Results  We sequenced the mitochondrial genomes of two sarcoptiform mites,  Histiostoma feroniarum  (13,896 bp) and  Rhizoglyphus robini  (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of  H. feroniarum  and  R. robini , respectively. The other six mt tRNA genes in  H. feroniarum  and five mt tRNA genes in  R. robini  can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in  St. magnus , two of the three mt tRNA genes that were reported as lost in  T. longior  and  T. putrescentiae , and the two mt tRNA genes that were reported as lost in  Sa. scabiei . All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems.    Conclusions  Our results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4868-6) contains supplementary material, which is available to authorized users.

The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?