A detailed knowledge of the geographical distribution of cytotypes within and between species comprising a polyploid complex is critical to our understanding of the history and evolution of such complexes. In the present study we examined the geographical distributions of cytotypes within six tentatively delimited species comprising the Chrysanthemum indicum complex in China. We determined the ploidy of 188 individuals sampled from 47 populations, based on DNA content using flow cytometry. In addition, chromosome counts were made on samples of each taxon. We confirmed that all samples of C. rhombifolium and C. lavandulifolium were diploid (2n = 18), those of C. hypargyrum and C. potentilloides were tetraploid (2n = 36), and those of C. vestitum were hexaploid (2n = 54). In contrast, we confirmed that C. indicum contained both diploid and tetraploid cytotypes. We found that in addition to marked differences in genome size between ploidy levels, there was a variation in genome size between species of the same ploidy level. Although the diploid, tetraploid, and hexaploid taxa of the complex, as well as the diploid form of C. indicum, occurred only in central and northern China, the tetraploid form of C. indicum was widespread both north and south of the Yangtze River. We suggest that the tetraploid form of C. indicum may have expanded its range southward during recent Quaternary glacial periods when forests retreated in south China as conditions became drier.