Abstract: Cobia Rachycentron canadum is the only species of Rachycentridae distributing widely in subtropical andtropical oceans and seasonally in temperate waters. Cobia has the qualities that define an excellent candidate andemerging global potential for mariculture. Numerous comparative studies have been conducted in attempt to resolve therelationship (to be monophyletic) between Rachycentridae and the other teleosts using anatomical and behavioralmethods. The Coryphaenidae and the Rachycentridae and Echeneidae were thought to form a monophyletic group, withCoryphaenidae being the sister group to the clade of Rachycentridae and Echeneidae. Nematistiidae and Carangidaewere also hypothesized to be part of a clade with these three families, perhaps forming a trichotomy. However, molecularresearch regarding the evolutionary relationship of these families remained scarce. Adequate resolution of relationshipsin any organisms required longer DNA sequences. In this study, the whole mitogenome sequence was determinedfor cobia, using an approach that employs a long polymerase chain reaction technique and primer walking. It was thefirst complete mtDNA sequence of cobia (Accession No. FJ154956 and NC_011219, 16758 bp) in GenBank. The mitochondrialgenomic sequence contained the same 37 mitochondrial structural genes (two ribosomal RNA, 22 transferRNA, and 13 protein-coding genes) as found in other vertebrates, with the gene order identical to that in typical vertebrates.All following analyses were based on two datasets. Dataset 1 consisted of highly similar DNA sequences of mitogenomes(score=10055-30213) from GenBank; and dataset 2 included the 20 ND2 gene complete sequences of therepresentative species within Coryphaenidae, Nematistiidae, Echeneidae and all branches with high support values in thetrees based on dataset 1. The phylogenetic relationship among cobia and other teleost were reconstructed using maximumparsimony (MP), neighbor-joining (NJ), and maximum likelihood (ML) with dataset 1. MP bootstrap scores weremuch lower than those of NJ or ML, and the MP resolution among higher-level classification were also the lowest.While the NJ and ML analyses provided strong support for a sister group relationship between two clades of Perciformes,in which one clade contained cobia, Carangidae (Carangoides armatus, Trachurus japonicas, and T. trachurus), Istiophoridae(Makaira indica, Istiophorus platypterus)and Xiphiidae (Xiphias gladius) (bootstrap=78 and 97). Unexpectedly,another clade was composed of the other taxa of order Perciformes and two typical species(Ostracion immaculatusand triacanthodes anomalus)of order Tetraodontiformes. The origin time of cobia was estimated by Bayesian analysis ofthe dataset 2 under the GTR+G+I+relaxed model for 8.0×106 generations resulted in a posterior probability distributioncontaining 1000 samples per analysis. The results support that: (1) the relative between cobia and dolphinfish is theclosest (posterior probability=0.997), and identical with the period of first occurrence of cobia fossil, their most recentcommon ancestor (MRCA) lived in 56 million years ago (Ma), i.e. Thanetian. (2) Rachycentridae, Coryphaenidae andEcheneidae of the superfamily Echeneoidea proposed by Johnson (1984) cluster in a monophyletic group with low posteriorprobability(0.593). However, Nematistiidae and Carangidae are placed in clusters of scombridae and Tetraodontidae,repectively. Conclusively, Carangoid lineage is not a monophyly.