Kumquats (Fortunella spp.) is classified into the subfamily Aurantioideae (family Rutaceae). The taxonomy and phylogeny of this genus are complicated and controversial. Therefore, we carried out a estimation based on chromomycin A₃ (CMA) karyotype composition in order to understand the cytogenetics and evolution of the genus Fortunella. Among the 6 Fortunella species examined, Fortunella hindsii var. chintou Swing. (Hongkong kumquat) showed the simplest CMA karyotype composition. On the other hand, close relationships were found among the 3 species F. margarita (Lour.) Swing. (Oval kumquat), F. japonica (Thunb.) Swing. (Round kumquat), F. crassifolia Swing. (Meiwa kumquat). Fortunella polyandra (Ridl.) Tan. (Malayan kumquat) and F. obovata hort. ex Tan. (Changshou kumquat) had type E chromosomes, which is an elemental chromosome type for Citrus. We concluded that there are only two true species for the genus Fortunella, F. hindsii and F. margarita complex, which includes F. margarita, F. japonica, and F. crassifolia, and that F. polyandra and F. obovata should be classified as natural or horticultural hybrids.