The present study investigated 5S and 45S rDNA sites in six Fritillaria species. All species were diploid with 2n = 2x = 24 chromosomes. One, three, or four B chromosomes (Bs) were detected in F. assyriaca ecotypes. Another two B- chromosomes were observed for F. zagrica. One to two pairs of 5S rDNA sites were observed in terminal or sub-terminal chromosomal regions. The number of 45S rDNA sites was one pair in F. raddeana, three in F. assyriaca, F. zagrica, and F. persica, four in F. avromanica, and eight in F. chlorantha. Most of the 45S rDNA sites were distal except for F. raddeana with a pair in interstitial and F. chlorantha with two pairs in sub-terminal locations. Chromosome and karyotype indices were identified, F. avromanica and F. chlorantha as the species with the most symmetrical and asymmetrical chromosomes, respectively. Cluster analysis of the karyotype similarity matrix showed that the number and distribution of the observed rDNA sites were not congruent with the taxonomy of species in the defined subgenus entirely. Particularly for F. chlorantha which belongs to the Fritillaria subg.