Chuzhou Crucian Carp (Carassius auratus in Chuzhou) is one of the natural gynogenetic crucian carp originated from Anhui Province in China. It belongs to the genus of Carassius within the family of Cyprinidae. To investigate the species status of this fish, we performed the direct DNA sequencing on the PCR products of the complete mitochondrial DNA (mtDNA). The total length of the mtDNA was 16581 bp, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding control region. The composition and location of genes in the mitochondrial genome of Chuzhou Crucian Carp were consistent with those of Cyprinidae fishes published in GenBank. The tRNA genes formed typical secondary structures except for tRNA-Ser (AGY). The COⅠ gene had GTG as its initiation codon, and the other 12 protein-coding genes had ATG as the initiation codon. Among the 13 protein-coding genes, 9 had complete stop codons but COⅡ, ND3, ND4 and Cyt b had an incomplete T as the stop codon. Sequence analysis showed that there was high similarity between the mtDNA sequences of Chuzhou Crucian Carp and other species in genus Carassius recorded in GenBank (>94%). The nucleotide composition of Chuzhou Crucaian Carp was 31.6% (A), 26.2% (T), 16.1% (G) and 26.2% (C). We conducted the phylogenetic analysis of the mitochondrial genomes of 9 Carassius fishes and 1 Cyprinus carpio, based on their nucleotide and amino acid sequences of all protein-coding genes. The results indicated that the phylogenetic relationship between C. auratus gibelio in Chuzhou and in Fangzheng was the closest while C. auratus gibelio in Chuzhou and Carassius carassius was the farthest. Our study may provide basic data and contribute to the classification of Carassius and Cyprinidae fishes.