Genetic diversity and evolutionary relationships of 72 accessions representing six species with the B-, C-, and BC-genomes in the genus Oryza were investigated by seven microsatellite markers. Of four diploid species, Oryza officinalis maintained the highest diversity (P=71.4%, He=0.565), followed by Oryza eichingeri (P=57.1%, He=0.376), Oryza punctata (P=57.1%, He=0.272) and Oryza rhizomatis (P=42.9%, He=0.222). In comparison, a higher level of genetic diversity was revealed in the tetraploid (P=71.4%, He=0.461-0.637). UPGMA dendrograms based on genetic distance revealed an obvious genetic differentiation between Asian and African races of O. eichingeri. Three BBCC species clustered with different accessions of the diploid O. punctata, suggestive of their multiple origins. The results inferred from the dendrogram suggested that diploid species, O. officinalis and African O. eichingeri might be the C-genome donors for tetraploid species, Oryza minuta and O. punctata, respectively, while the C-genome ancestor of Oryza malampuzhaensis seemed to be either O. rhizomatis or the Sri Lankan O. eichingeri species. The genetic relationship among the CC and BBCC species further indicated that the tetraploid species with the BC-genome have originated independently, at least three times in history. In addition, we have demonstrated successful cross-species amplification of seven rice SSR loci across Oryza species with B-and C-genomes.