In the present study, the complete mitochondrial genome of the oval flounder Bothus myriaster was determined and a novel gene rearrangement was discovered. A striking finding was that eight genes encoded by the L-strand (ND6 and tRNA-Q, A, C, Y, S1, E, and P genes) were translocated to a position between tRNA-T and tRNA-F. Simultaneously, the original order of the rearranged genes Q-A-C-Y-S1-ND6-E-P was maintained. Thus, the genes with identical transcriptional polarities were clustered in the genome with one exception that tRNA-N gene is located in the original position. The other rearrangement was the H-strand-encoded tRNA-D that translocated from its typical location between COI and COII to a position between S1 and ND6. The Dimer-Mitogenome and Non-random Loss model (DMNL)was adopted to account for the novel rearrangement in B. myriaster mitogenome, which provides evidence to support the hypothesis of the DMNL model.