The suborder Stromateoidei (Teleoste: Perciformes) currently comprises 6 families, 16 genera, and about 70 species. They occur worldwide in coastal and oceanic waters of tropical to temperate regions. Fishes of Stromateoidei are one of the most economically important in the world. However, due to the highly diversity of morphological characters, the taxonomic status and phylogenetic relationships of Stromateoidei has been long-lasting confused. In this study, the mitochondrial 16S rRNA gene fragment of 8 species of Stromateoidei collected from Chinese coastal waters, were amplified using PCR techniques. The homologous sequences of other Stromateoidei fishes from GenBank were also included in this study. The genetic information indexes, including base composition, sequence variation and Kimura-2 parameter genetic distance were examined. Phylogenetic trees were constructed based on neighbor-joining (NJ) and maximum-parsimony (MP) methods. Of the 458 aligned base pairs, with 119 variable sites, 114 parsimony informative sites, 5 singleton sites, were detected in the analyzed Stromateoidei fishes (5 families, 13 genera, and 32 species). The average contents of T, C, A and G were 22.2%, 24.5%, 30.0% and 23.3% respectively for COI analysis. The genetic distances among families, genera and species were respectively range from 0.060 to 0.120, 0.009 to 0.125, and 0.000 to 0.163. The phylogenic analysis placed Centrolophidae in the most basal position of the Stromateoidei, Pampus (Stromateidae) at the top of the two trees, Ariommatidae, Tetragonuridae, Nomeidae in a sister position to the clade of Peprilus and Stromateus (Stromateidae). Based on the results of molecular analysis and morphology data, the several conclusions were drawn as follow: (1) family Centrolophidae, which was early diverged, is the most primitive monophyly group in the suborder Stromateoidei; (2) Ariommatidae, Tetragonuridae are the two monophyletic groups, which showed close relationship with the non-monophyletic group of Nomeidae; (3) the paraphyletic group of Pampus is the most recently diverged species, which is in accordance with the fact that it is also the most flourishing genus in Stromateoidei. There are two parallel evolutionary clades in genus Pampus. The species within the two clades seem to be relevant to their biogeographic distributions. In addition, the application of 16S rRNA gene for phylogenetic study in the suborder Stromateoidei is discussed in this study.