The rice C0t-1 DNA and genomic DNA were used as probes to comparatively analyses Oryza.Sativa,O.punctata and O.brachyantha genome by fluorescence in situ hybridization(FISH).The results showed that C0t-1DNA mainly distributed on centromere,acrocentric and telomere,and there were much more signals on chromosomes in O.punctata than that of in O.brachyantha.This was consistent with that of FISH using gDNA as probe,indicating the relationship between genome A and genome B is much closer than that of between genome A and genome F.The feasibility of the investigation of relationships between species in the genus was confirmed by using highly and moderately repetitive DNA sequences,C0t-1DNA.At the same time,karyotype analysis of O.punctata and O.brachyantha were carried out based on C0t-1 DNA hybridizational signal bands.