The entire mitochondrial DNA sequence(mitogenome)of five species,Lutjanus bengalensis, Lutjanus malabaricus, Lutjanus sebae, Lutjanus kasmira and cobia(Rachycentridae:Rachycentron canadum)were determined using long PCR and primerwalking methodology with universal primers,and their GenBank Accession numbers are FJ171339,FJ416614,FJ824741,FJ824742 and NC_011219,respectively.The mitochondrial genomic sequence in snappers and cobia are similar to other vertebrate mitochondrial genomes with respect to gene order and genomic organization.Phylogenetic relationships derived from mtDNA sequences of Lutjanus russellii, Lutjanus rivulatus, Lutjanus bengalensis, L.malabaricus, L.sebae, L.kasmira, cobia and dark banded fusilier(Caesioninae:Pterocaesio tile)were incongruent with those derived from morphological taxonomic analyses.Beyond expected,high homogeneities were observed between some lutjanids and fusilier,belonging to Lutjaninae and Caesioninae.Further efforts may clarify the phylogenetic relationships among these snappers.Moreover,we investigated the performance of all thirteen mitochondrial proteincoding genes to recover the phylogenies.According to these tests,mitochondrial proteincoding genes can be roughly classified into four groups at the level of genus:of very good(ATPase6 and cox2),good(cox1 and ND2), medium(cox3, NDl, ND4, ND4L and ND5),and poor(ND3, ND6,and ATPase8).And we inform that simple length differences and rate differences between these genes cannot account for their different phylogenetic performance.We advice the careful selected genes and their combinations should be helpful for high resolved phylogenetic analysis for different level taxon.