In order to explore the molecular cytogenetic evidence of the relationship and phylogeny of genus Rosa, we located and analyzed the 45S and 5S rDNA of 17 species from 7 sections in China by using the technique of twocolor FISH (fluorescence in situ hybridization). The results suggested that: (1) one set of chromosomes corresponded to one 45S rDNA locus (except R. brunonii, which corresponded to two 45S rDNA), and one or two 5S rDNA loci. (2) At least one pair of 5S rDNA signals were colocated with 45S rDNA signals in diploid rose species, while 5S rDNA signals did not collocated with 45S rDNA signals in all of the tetraploid species; However, all tetraploid materials had at least one kind of rDNA signal homozygosity, indicating that they should be homologous tetraploid generated by direct doubling of diploid. (3) R. roxburghii f. roxburghii (sect. Microphyllae) was more distantly related to other species of Rosa, because it had a 5S rDNA signal on the short arm of the chromosome, unlike other species of _Rosa.(4) The karyotype as well as the numbers and locations of 45S and 5S rDNA were different in Aksu region and Yili region. The molecular cytogenetic evidence supported that R. laxa in Aksu region should be a new variety of the R. laxa. (5) To the best of our knowledge, the twocolor FISH analyses of tetraploid roses (6 taxa) and 8 diploid taxa has been reported for the first time in this study. The study provided that the heterologous chromosomes, differences of positions of rDNA signals on homologous chromosomes and the increase and loss of rDNA signals in both diploid and tetraploid plants in Rosa may be related to the structure variation and recombination of chromosomes. The structure variation and recombination of chromosomes were proved to played an important role in the evolution of Rosa at the level of molecular cytogenetics.