Mitochondrial DNA(mtDNA) was obtained from livers and ovaries of Carp (Cyprinus carpio) and Crucian carp (Carassius auratus) using an improved method. The mitochondrial genomes from Carp and Crucian Carp consist of 16.99 kbp and 16.30 kbp, circular DNA respectively. By means of 7 different restriction endonucleases their mitochondrial DNA physical maps were constructed. It was found that the length and restriction sites of the specific mitochondrial DNA show relative stability. Restriction endonuclease analysis of mitochondrial DNA of triploid hybrid between Crucian Carp and Carp reveals that the hybrid mitochondrial DNA appears to be same as that of maternal Crucian Carp. A series of small DNA, size between 300 bp to 6000 bp, were found in hydrid mitochondria, but it was never detected in parental individuals. The origin and function of this kind of DNA, tentatively named heterogeneous small mitochondrial DNA (hs-mtDNA), are unknown and remained to be studied.