Korean Chrysanthemum species naturally distributed throughout Korea is regarded as one of the most popular ornamentals and medicinal herbs. Phylogenetic studies were conducted to evaluate interspecific relationships in 19 populations of Korean Chrysanthemum species including 16 taxa and two outgroups using internal transcribed spacer (ITS1, ITS 2) region sequences of nuclear ribosomal DNA (nrDNA) and chromosome number. Phylogenetic analysis was conducted using strict consensus methods. The taxa have well-developed series of polyploids (4x, 6x, 8x) from diploids (2x) with basic chromosome number (n = 9). The length of ITS sequences aligned was 663–664 bp, and the length of ITS 1 and ITS 2 regions were 268–269 bp and 231 bp, respectively. The divergence rate was very low within Chrysanthemum zawadskii subspecies from 0.0 to 1.4%. In the phylogenetic tree obtained by strict consensus analyses, the taxa were divided into three major groups. The C. lineare appeared as the most basal clade within the Korean Chrysanthemum. This result suggest that Chrysanthemum morphologically independent group such as C. zawadskii and C. indicum subspecies were unresolved with ITS region sequences. These findings contribute to our understanding of the phylogeny, origin, and classification of Chrysanthemum species. Chrysanthemum species could have been derived from the same ancestor to advance polypoidy for the phylogenetic analysis based on ITS sequence and chromosome data.