Molecular cytogenetics opens an avenue to address old questions of biosystemtics and new questions of genome evolution. Genomic in situ hybridization (GISH) was used to examine origins and evolution of the allotetraploid genomes, BBCC and CCDD, of Oryza (Poaceae). The results indicated that species of the BBCC genome contained two clearly distinguishable diploid genomes of BB and CC. The CCDD genome, which had a more ancient origin than the BBCC genome, has undergone extensively DNA exchange between chromosomes of the two diploid genomes. The dispersed hybridization signals consequently prevented the detection of the allotetraploid origin of the CCDD genome using GISH. The strength of GISH signals between various diploid genomes of Oryza was often inconsistent with phylogeny or sequence divergence of single-copy nuclear genes. This raises an important question concerning genomic and evolutionary interpretation of GISH results.

Key words: allopolyploid, genome evolution, GISH, Oryza