The predatory mite Cheyletus malaccensis (Acari: Cheyletidae), commonly occurring in stores of various food commodities, is an important natural enemy of stored product pests. Disentangling the mt genome sequence of C. malaccensis at molecular level can decrease uncertainties during morphological identification and is useful in reconstructing the phylogeny of Acariformes group. In this study, the complete mitogenome of C. malaccensis was sequenced by the next-generation sequencing. After assembly and annotation, we found the circular 14,732 bp mitogenome of C. malaccensis, containing 13 protein coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Compared with the ancestral mitogenome organization of arthropods, most of tRNA were truncated without D-arm or/and TψC-arm. Rearrangement was found in 12 mitogenome genes. Phylogenetic analyses based on the mitogenome data from other 29 mite species were inferred by Bayesian and maximum likelihood methods, which strongly supported the closer relationship between C. malaccensis and Tetranychidae than other mites. The obtained results represent the first complete mitochondrial genome record for Cheyletidae group. It may help improve molecular phylogenetic relationship and population genetics of the Cheyletidae.