Mitochondrial DNA (mtDNA) heteroplasmy has been found to be commonly present in many organisms. However, the studies on the mitochondrial heteroplasmy within group of fishes are currently lacking. This specific purpose of this study was to investigate the mtDNA heteroplasmy in different organs within group of common carp. Based on cytochrome B (cyt B) gene, we amplified in a fragment of cytB gene from three tissues including liver, kidney and muscle of five individuals via polymerase chain reaction (PCR) with Pfu DNA polymerase, sequenced the amplified DNA fragments and compared mitochondrial heteroplasmy among these tissues. The result showed that the mean frequency of wild-type in muscle, liver and kidney was 54.4%, 56.8% and 68% respectively. Among the point mutations, frequency of substitution of G for A and C for T is 58.2%, 71.4% and 74.1% respectively in muscle tissues, liver and kidney.