In this study, the complete mitochondrial genome of Ophichthus evermanni was obtained by high-throughput sequencing. The results of structure and characteristics analysis showed that the total length of the complete mitochondrial DNA was 17759 bp, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), 2 ribosomal RNAs (rRNA), 2 control regions (D-loop), and 1 origin of the L-strand replication region (OL). The base composition of the complete mitogenome of O. evermanni was A (31.27%), G (16.19%), C (26.22%), and T (26.32%). The A+T content (57.59%) was greater than the G+C content (42.41%), showing an obvious A+T bias. Unlike other typical teleosts, the gene arrangement was identified in the mitogenome of O. evermanni. The ND6 gene and the conjoint tRNA-Glu were translocated between tRNA-Thr and tRNA-Pro, and another highly homologous D-loop region was located upstream of the ND6 gene. The tRNA-Gln (Q), tRNA-Ala (A), tRNA-Asn (N), tRNA-Cys (C), tRNA-Tyr (Y), tRNA-SerUCA (S1), tRNA-Glu (E), tRNA-Pro (P), and ND6 were located in the L-strand, whereas the remainder were located in the H-strand. Except for tRNA-Ser (AGC), the remaining 21 tRNAs could fold into the typical cloverleaf secondary structure. The phylogenetic relationships of Ophichthidae fishes were constructed based on 12 protein-coding genes (excluding ND6) using the neighbor-joining and Bayesian methods. The results suggested that O. evermanni was closely related to O. brevicaudatus and Pisodonophis cancrivorus, and genetic divergence occurred in the genus Ophichthus, which was relatively late among the family Ophichthidae. The results will supplement the mitochondrial genome database of the family Ophichthidae and also provide a reference for the taxonomic study of snake eels.