[Objectives]  The Anoplura are sucking lice; obligate, hematophagous ectoparasites of eutherian mammals and potential vectors for pathogens that can cause severe infectious diseases in humans and other animals. The mitochondrial genome of the Anoplura is distinct from the traditional understanding of that of a bilateral animal. Extensive fragmentation is present in the mt genome forming multiple mini-circular mitochondrial chromosomes. Although a revision of the taxonomic status of the Anoplura is urgently required, there has so far been very little phylogenetic analysis of the group based on 16SrRNA sequence variation and mitochondrial genome fragmentation. [Methods]  Phylogenetic relationships were inferred by comparing 16SrRNA gene sequences of 13 species from 6 genera and 6 families using the arithmetic mean (UPGMA), neighbor-joining (NJ) and maximum parsimony (MP), methods. The mitochondrial genomes of 4 species in 2 genera and 2 families were sequenced using the Illumina Hiseq 2000 platform, and the extent of mitochondrial genome fragmentation in 10 species from 5 genera and 5 families was analyzed. [Results]  A phylogenetic tree supports the current morphological taxonomy in that the 6 families are monophyletic and the Pedicinidae the most primitive. The analysis of the extent of mitochondrial genome fragmentation in 10 species from 5 genera and 5 families shows that the 3 species of human lice (Pediculus humanus, Pediculus capitis and Pthirus pubis) are more fragmented than the 4 species of rat lice (Polyplax asiatica、Polyplax spinulosa、Hoplopleura kitti and Hoplopleura akanezumi). The 3 species of Haematopinus lice (Haematopinus suis, Haematopinus apri and Haematopinus asini) have the least degree of fragmentation. The phylogenetic tree indicates that the relative degree of evolutionary divergence can be ranked as: Haematopinus lice < rat lice < human lice, which is consistent with the extent of mitochondrial genome fragmentation from slow to fast. [Conclusion]  A phylogenetic tree of the Anoplura based on variation in 16SrRNA gene sequences indicates that different lineages are basically monophyletic, and supports the current morphological taxonomy. The level of mitochondrial genome fragmentation in the Anoplura may be consistent with the divergence of taxa.