[Objective] This study was to explore the relationship of genomes between Oryza alta and Oryza latifolia using genomic in situ hybridization.[Method] Total DNA of C-genome was used as a probe for genomic in situ hybridization with metaphase chromosome from Oryza alta and Oryza latifolia,respectively.[Result] Under certain elution stringency,C-genome and D-genome could be distinguished in CCDD genome type;there were huge differences between some CC-genome in Oryza alta and Oryza latifolia,and the genome of Oryza latifolia was more original.[Conclusion] Comparative analysis of the Oryza species with identical genome type may facilitate to elucidate the possible approaches to plant genome evolution and species evolution.