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The complete mitogenome sequence of the flea, Hystrichopsylla weida qinlingensis (Siphonaptera: Hystrichopsylla) was sequenced. The 17,173 bp long genome has the standard metazoan complement of 37 genes. These genes contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The nucleotide composition of the H. weida qinlingensis mitogenome was A: 39.10%, T: 41.49%, G:7.56%, and C: 11.85%. The A + T content is 80.59%, showing strong AT bias. Phylogenetic analysis indicates that Hystrichopsylla has a close affinity with a branch of Dorcadia.