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The mitochondrial genome structure of a teleostean group is generally considered to be conservative. However, two types of gene arrangements have been identified in the mitogenomes of Anguilliformes. In this study, we report the complete mitochondrial genome of <i>Ariosoma meeki</i> (Anguilliformes (Congridae)). For this research, first, the mitochondrial genome structure and composition were analyzed. As opposed to the typical gene arrangement pattern in other Anguilliformes species, the mitogenome of <i>A. meeki</i> has undergone gene rearrangement. The <i>ND6</i> and the conjoint <i>tRNA-Glu</i> genes were translocated to the location between the <i>tRNA-Thr</i> and <i>tRNA-Pro</i> genes, and a duplicated D-loop region was translocated to move upstream of the <i>ND6</i> gene. Second, comparative genomic analysis was carried out between the mitogenomes of <i>A. meeki</i> and <i>Ariosoma shiroanago</i>. The gene arrangement between them was found to be highly consistent, against the published <i>A. meeki</i> mitogenomes. Third, we reproduced the possible evolutionary process of gene rearrangement in <i>Ariosoma</i> mitogenomes and attributed such an occurrence to tandem repeat and random loss events. Fourth, a phylogenetic analysis of Anguilliformes was conducted, and the clustering results supported the non-monophyly hypothesis regarding the Congridae. This study is expected to provide a new perspective on the <i>A. meeki</i> mitogenome and lay the foundation for the further exploration of gene rearrangement mechanisms.