Variations existing in protein-coding genes of the complete mitochondrial genomes of two highly morphological similarity fish: and (Perciformes, Gobiidae).

is a new record species of Gobiidae in China. It had been misidentified as for long time early before 2006. Here, the complete mitochondrial genome (mtDNA) sequences of the two species were first reported and analyzed comparably. The two genomes were both consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. It was 16,496 bp and 16,803 bp, respectively, and had a 238 bp-gap between tRNAleu and ND5. There were high variations (10-19%) in the protein-coding genes. In the initiation condon and stop codons, the two fish also had tiny difference. Phylogenetic analysis showed that and first clustered together and then they constituted Gobiidae clade with other 12 fish. Whereas Odontobutidae and Rhyacichthyidae formed the sister group, then clustered with Eleotridae, and finally joined with Gobiidae, which is consist with previous phenotypic report. The study will contribute to the phylogenetic analysis of the Gobiidae and natural resources conservation of and .