An improved fluorescence in situ hybridization (FISH) method for localizing genes and DNA sequences on rice chromosomes has been developed in our laboratory. Three improvements in the fluorescence in situ hybridization procedures, i.e. development of four steps of posttreatments, development of a modified thermal cycler and introduction of an imaging method enabled to obtain clear and reproducible signals on rice chromosomes. The improved FISH method was employed for physical mapping of 45S ribosomal RNA genes in Oryza species. Variability in the number of 45S rDNA loci was detected among eight diploid species. The FISH method was also applied to localize the rice repeated sequences. The repeated sequences were adjacent to the telomeric regions of the long arms of chromosomes. Furthermore, a multicolor FISH (McFISH) method was developed and was applied to characterize O. glaberrima chromosomes.