The three croakers (Nibea coibor, Protonibea diacanthus and Argyrosomus amoyensis, Perciformes, Sciaenidae) are important commercial species inhabiting the Eastern Indian Ocean and Western Pacific. Molecular data employed in previous research on phylogenetic reconstruction have not been adequate and complete, and systematic and comprehensive phylogenetic relationships for these fish are unresolved. We sequenced the complete mitochondrial genomes of the three croakers using next-generation sequencing for the first time. We analyzed the composition and phylogenies between 19 species in the family Sciaenidae using the mitochondrial protein coding sequences of 204 species in the Series Eupercaria. We present the characterization of the complete mitochondrial genome sequences of the three croakers. Gene arrangement and distribution of the three croakers are canonically identical and consistent with other vertebrates. We found that the family Sciaenidae is an independent branch that is isolated from the order Perciformes and does not belong to any extant classification. Therefore, this family is expected to belong to a new classification at the order level and needs further analysis. The evolution of Sciaenidae has lagged far behind the Perciformes differentiation. This study presents a novel insight into the phylogenetics of the family Sciaenidae from the order Perciformes and facilitates additional studies on the evolution and phylogeny of Series Eupercaria.

We present the complete mitochondrial genome of the Clarias fuscus in this study. The mitochondrial genome is 16,525 bp in length and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 31.17% of A, 27.54% of C, 25.34% of T, and 14.95% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. All the protein-coding genes begin with an ATG initiation codon except for COXІ with GTG. Five types of termination codons revealed are TAA (COXІ, ATP8, ND4L), T (ND2, ND3, ND4, COXП, Cytb), AGG (COXШ), TA (ATP6), and TAG (ND1, ND5, ND6). Most genes are either abutted or overlapped and many features keep consistent with the other vertebrates.

We present the complete mitochondrial genome of the Plectorhinchus cinctus in this study. The mitochondrial genome is 16,523 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 31.30% of C, 27.66% of A, 24.54% of T, and 16.50% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. All the protein-coding genes begin with an ATG initiation codon except for COX1 with GTG. Five types of termination codons revealed are TAA (ND1, ND2, ATP8, ND4L, ND5), T (COXП, ND3, ND4, CYTB), TA (ATP6, COXШ), AGG (COXІ) and TAG (ND6).