Cypriniformes is the largest order of freshwater fishes. The phylogenetic relationships of the Cypriniformes have been studied by many investigators based on morphological characters, but no agreement has been reached. In the present paper, complete mitochondrial 12S rRNA sequences of five families of the Cypriniformes were determined and analyzed to test the present morphological hypotheses. After alignment, there are 1 000 sites, among which 467 sites are in steins and 533 sites in loops. 395 sites are variable, and of which 267 are informative. Neighbor-joining and Maximum Parsimony methods were employed for phylogenetic analysis. The results indicate that the cyprinids form a monophyletic group while the non-cyprinid cyprinifonns form another one, which is in accordance with the hypothesis proposed by Siebert. The Cyprinidae consists of three main clades, the Danionini, the Cyprinini, and the Leuciscini. However, in the non-cyprinid cyprinifonns, the relationships could not be resolved clearly. The Cobitidae is polyphyletic. Homalopteridae, Noemacheilinae and Cobitinae may have closer relationships.