The complete mitogenome of natural triploid Carassius auratus in Qihe River. 
Qihe Carassius auratus is the territorial Carassius auratus, which is known as for its limited distribute in Qihe River (mainly distributed in Henan province, China), this species is natural triploid in China.  In this study, the complete mitochondrial genome sequence of Carassius auratus in Qihe River has been obtained with PCR.  The gene composition and arrangement of mitochondrial genome sequence of this species are similar to most of other vertebrates', which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and a non-coding control region with total length of 16,580 bp.  Most of genes are encoded on Heavy-Strand (H-strand), exclude eight tRNA and ND6 genes, which are encoded on Light-Strand (L-strand).  The bias of G and C has been found in different regions/genes and different statistic results.  The complete mitochondrial genome sequence of this species would contribute to better understand population genetics, conservation, and the evolution of natural triploid.