The mitochondrial DNA control region of 12 finless porpoises (Neophocaena phocaenoides) from the Yangtze River, Yellow Sea, and South China Sea, was amplified. Two portions, 317 and 245 base pairs, respectively, were directly sequenced to characterize the amount of genetic variation of finless porpoises in Chinese waters. No haplotype was shared among the Yangtze River population, the Yellow Sea population, and the South China Sea population. The phylogenetic trees using the two nucleotide sequences, as well as a longer sequence (562bp) formed by combining the former two sequences, clustered the haplotypes into three clades corresponding to the three geographical populations. The levels of genetic differentiation within each population were much lower than those between populations, indicating that the populations have diverged and are probably reproductively isolated. Because of the obvious genetic differentiation among the three populations, they should be regarded as different population units in their conservation and management.