Abstract: Many informative fragments of the RAPD were obtained from 30 individuals that representing 20 species of the primitive cyprinid fishes by the method of random amplifying with 20 primers. We converted the DNA polymorphic fragment into genetic distance by the program Rapdplot (d=1-S, S=2NxNy/Nx+Ny). The prograxns Neighbor in software package PHYLIP was used to calculated the matrix of genetic distance resulted which in one cladogram of 20 species. It is indicated that the application of the RAPD analysis for Cyprinidae may have some limitations. For the inter-genera analysis in same subfamily, the result is reliable. The result of the RAPD analysis indicates that: the subfamily Danioinae is not a monophyletic group.Among them, the Zacco group and Aphyocypris group form monophyly respectively. And in this subfamily, the two groups do not have a direct relationship.