Using the method of double color fluorescence in situ hybridization (FISH), we had analyzed Triticum polonicum L. and T. turgidum L. cv. Ailanmai with the probes of 45S rDNA and 5S rDNA. The results indicated that there were highly consistent in T. polonicum L. High and T. turgidum L. cv. Ailanmai, both having four 45S rDNA loci and six 5S rDNA loci. In T. polonicum L. Dwarf, there were also four 45S rDNA loci, the same as that in T. polonicum L. High and T. turgidum L. cv. Ailanmai, but there were eight 5S rDNA loci. At the same time, we discussed the reason of interspecific and intraspecific variation of the two types of rDNA in locus number and location between T. polonicum L. and T. turgidum L. cv. Ailanmai.