Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.Keywords: Acipenseriformes, mtDNA ND4L, mtDNA ND4, molecular phylogeny, DNA sequencing.Sturgeons and paddlefishes, which belong to the order Acipenseriformes, are the endangered primitive fishes. This group of fishes occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution, on the other hand, the populations of sturgeons and paddlefishes worldwide have declined [1] . Though Acipenseriformes has long been regarded as an interesting group in biogeographical and phylogenetic studies since the times of Linnaeus, the classification of the fishes has been controversial. So far, the phylogenetic studies of the group remain in their infancy [2] . There are about 27 extant species worldwide. However, the exact number of species and systematic relationships among different genera and different species are still unknown. Though some data on morphology, cytogenetics and molecular biology have been accumulated, there is still a long way to go to fully understand the phylogenetic relationships.DNA is an honest recorder of evolutionary history of organisms. Studies on DNA sequences