Chrysanthemum is a valuable ornamental plant worldwide, and several of its species are used as herbal tea, medicinal plants, and dietary supplements, among others. Commercial cultivars have been developed through interspecific hybridization and artificial selection to improve the characteristics, production quality, and environmental adaptation for enhancing ornamental value. To better understand the recent research in cytogenetic studies of chrysanthemum, we examined studies concerning polyploidy, karyotyping, banding, fluorescence in situ hybridization (FISH) technique, and inter/intraspecific hybridization. Ploidy level is important in genomic characteristics and has a significant value to horticulturists and plant breeders. Studies have reported that flow cytometry analysis and single-dose molecular markers can be used to determine the chrysanthemum ploidy level. As for karyotyping, a better understanding of karyomorphological relationships and evolution of chrysanthemum and its closely related genera has already been gained. Moreover, karyotype parameters in chrysanthemum studies play a critical role in cultivar identification, classification, and genetic analysis. The FISH technique in chrysanthemum research provides more information on chromosome identification, sequences distribution, and evolution for expediting the development and improvement of plant species. The genomic in situ hybridization (GISH) technique can also be used to test hybridization in chrysanthemum breeding. Hence, this review of molecular cytogenetic studies of chrysanthemum will help us to have a better understanding and knowledge of the taxa breeding and the development and improvement of new cultivars.