The complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus, which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,882 bp in size and encoded of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Nemipterus furcosus has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that N. furcosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for addressing taxonomic issues.

The complete mitochondrial genome of Pentapodus setosus which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,836 bp in length with 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that P. setosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for resolving the taxonomic issues.

The complete mitochondrial genome of the Nemipterus virgatus has been sequenced. The mitochondrial genome is 16 992 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region. The gene order and composition of N. virgatus mitochondrial genome was similar to that of most other vertebrates. The overall nucleotides base composition of the light strand is A (27.89%), G (26.61%), C (16.45%), T (29.05%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, N. virgatus, Nemipterus japonicus, and Nemipterus bathybius from the same genus clustered into one branch.

The complete mitochondrial sequence of the Japanese threadfin bream, Nemipterus japonicus has been determined. The circle genome is 16,995 bp in size, and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of N. japonicus was similar to that of most other teleosts. The base composition of H-strand is 28.11% (A), 28.02% (T), 16.64 % (G) and 27.24 % (C), with an AT content of 56.12%. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of N. japonicus presented will be in favor of resolving phylogenetic relationships within the family Nemipteridae and the Perciformes.