Abstract: Generally, the mitochondrial genome is characterized by the property of highly conserved organization. After comparing the 1,255 fish complete mitogenome sequences deposited in GenBank (as of Nov. 3, 2013), approximately 52 complete mitogenomes are found to have been rearranged. Of these species, three types of rearrangement-shuffling, translocation, and inversion-have been found. Further analysis shows that the sites of the rearrangements occur frequently in WANCY cluster, IQM cluster, ND6 gene, control region (D-loop) and its adjacent genes. Based on the four models that explain the gene rearrangements commonly adopted by scientists, we attempted to infer the possible mechanisms for the three types of gene rearrangement as well as the application of gene rearrangement in phylogenetic studies.