The mitochondial cont rol regions from 13 st riped dolphins (S tenella coeruleualba), seven from the southern Taiwan St rait s (Dongshan waters) and the other six from the southern East China Sea (Pingtan waters), were amplified by using polymerase chain reaction (PCR) technique. The complete nucleotide composition of this region, ranged from 914 to 917 base pairs (bp), were determined by an ABI 310 DNA automated sequencing system to address the sequence variability. 42 variable sites, including 36 transitions, three t ransversions, and three indels (insertion/ deletion) were found. Of the variable sites, 26 were parsimonious informative sites. Totally 11 haplotypes were identified. Of the haplotypes, six were found exclusively in Dongshan waters and the rest five only in Pingtan waters. No common haplotype was shared, and two fixed site differences were detected between haplotypes from two waters. The haplotype diversty and nucleotide diversity were high for both waters, which were 1.45% ±0.79% and 0.95 in Dongshan waters, and 1.06% ±0.51% and 0193 in Pingtan waters respectively. A phylogenetic t ree was reconst ructed by using neighbor-joining (NJ) method in MEGA (Molecular Evolutionary Genetic Analysis) package. In the t ree, haplotypes from the Pingtan waters constituted a monophyletic clade, whereas haplotypes from the Dongshan waters did not. Analysis of molecular variance, which was conducted by computer software AMOVA, showed an significant population differentiation and genetic st ructure (Φst =0.35, P<0.01) between Dongshan waters and Pingtan waters. The haplotype diversity and nucleotide diversity of st riped dolphins were higher than those found in the sympat ric finless porpoise (Neophocaena phocaenoides) populations, and also higher than those of other cetacean species reported previously in other waters, including some species having high level of genetic diversity, e. g. harbor porpoises (Phocoena phocoena), humpback whales (Megaptera novaeangliae) and bottlenose dolphins (Tursiops spp.) etc. This suggested that the st riped dolphins had a relatively higher genetic diversity.