45S rDNA probes were used to analyze Oryza alta and O.latifolia both having CCDD genomes with fluorescence in situ hybridization.The results showed that the hybridization signals of 45S rDNA in O.latifolia chromosome preparations were distributed on different chromosomes with the number of 10-16.The same signal in O.alta chromosome preparations was 6 and distributed on the certain three pairs homologous chromosomes,with two pairs in short chromosome arms and the other one pair in long chromosome arm.The number and position of 45S rDNA signals were stabled in O.alta genome,but there were some dynamic changes of signals in O.latifolia genome.It is indicated that there were differences between these two kinds of CCDD genomes.Comparatively analyzing the karyotype of O.alta chromosomes and O.latifolia chromosomes based on the fluorescence in situ hybridization pictures showed that there were greater differences.It is proposed that O.alta maybe differentiate earlier and tend to be stable,while O.latifolia may be still in its evolutionary process.Based on the imbalance of evolution and differences of genomic structure,O.alta and O.latifolia were divided into two wild rice species,which may be well conformed with their evolutionary characteristics.The mechanism and characteristics of 45S rDNA’s distribution in the chromosomes were discussed.