Chrysanthemums (Asteraceae) are important ornamental crops in worldwide that are well known as commercial valuable cultivars for cut flowers, potted plants, and garden flowering plants. Genus chrysanthemum consisted of 41 species that are mostly distributed in East Asia. Chrysanthemum has diverse ploidy levels with the basic chromosome number of x=9 from 2n=2x=18 (diploid) to 2n=10x=90 (decaploid). Fluorescence in situ hybridization (FISH) is a useful tool for studying the distribution of ribosomal DNAs. In this study, we have confirmed ploidy level by chromosome counting method. The somatic metaphase chromosome numbers were observed 2n=2x=18 in Chrysanthemum boreale, and 2n=6x=54 in C. indicum and C. zawadskii. More detailed Karyotype was constructed based on FISH method using 5S and 45S rDNA probes. Two (2) loci of 5S rDNA signals were detected in interstitial region of long arm chromosome in C. boreale and six (6) loci were in C. indicum and C. zawadskii. All of 45S rDNAs were located in terminal region of short arm chromosome which were visualize in six (6) loci in C. boreale and C. indicum and twelve(12) loci in C. zawadskii. In this study, it was the main topic to perform physical mapping of the location of 5S and 45S rDNA. Three of wild chrysanthemum showed variations in number of ribosomal DNAs. In the present investigation will help to further study of genome sequencing project in chrysanthemum.