The D-loop of mitochondrial DNA from Chinese sturgeon (Acipenser sinensis) was amplified using PCR. The length variations among individuals and within individual (heteroplasmy) were detected. DNA sequence analysis revealed that interindivadual and intraindividual length variation occurred within D-loop near tRNA(pro), and caused by tandam repeat with 82 bp in length. Out of 47 individuals, 27(57.4%) individuals were heteroplasmy whereas 20 individual (42.6%) were homoplasmic. The length variation was also found among homoplasmic individuals. In homoplasmic individual four different size classes (number of tandem repeats) e.g. 2, 3, 4 or 5 repeats were noted. The frequencies of size classes from the highest to the lowest were 3-->2-->4-->5. In heteroplasmy two molecular size classes coexisted in an individual was most common (77.78%). The second type of heteroplasmy was three size classes coexisted (18.52%) and the lowest one was four size classes together in an individual (3.70%). No five different size classes coexisted in an individual was found. Through densitometry of DNA bands the frequencies of mtDNA size classes were determined for the sample of individuals, and the frequency distribution of repeats from the highest to the lowest was similar to that in homoplasmy (3-->2-->4-->5-->1). The diversity within each heteroplasmic individual was carried out and genetic diversity at hierarchical level was analyzed. 65.3% of genetic diversities were from among individuals in population and 34.7% of genetic diversities were from within individual. The mtDNA length variation within individual (heteroplasmy) is another genetic diversity resource for Chinese sturgeon.