Abstract: Fortunella is one group of the citrus fruit trees in southern China, a kind of edible hesperidium with rich flavonoids, carotenoids, limonoids, coumarins, and the fruit of these evergreen trees also have ornamental value. In recent years, areas of growth of commercial species of Fortunella have been decreasing due to a low net interest of planting single species. Meanwhile, natural resources have also withered due to the Huanglong disease caused by gram-negative bacteria. National collection of germplasm resources of Fortunella has been completed in parts of China, including Hunan, Fujian, Guangxi, etc.; however, this work did not take the effects of climatic factors on their distribution into consideration, which could provide a scientific basis for protection and collection of natural resources of Fortunella species. In this study, we predicted suitable climatic areas for six species (F. hindsii Swingle, F. margarita Swingle, F. japonica Swingle, F. polyandra Tanaka, F. crassifolia Swingle, and F. obovata Tanaka) of Fortunella using the MaxEnt (the maximum entropy, MaxEnt 3.3.3) model and the ArcGIS (the geographic information, ArcGIS 10.3) system to analyze actual geographical distribution data and 18 climate factors affecting their distribution. The dominant climate factors were screened through Jackknife test. Results showed that the suitable climatic region for the six species analyzed were distributed mainly in the southern areas of Dabie—Daba Mountain. The suitable region for the six species covered 354 000 km² (F. hindsii Swingle), 276 100 km² (F. margarita Swingle), 495 800 km² (F. japonica Swingle), 613 600 km² (F. polyandra Tanaka), 474 400 km² (F. crassifolia Swingle), and 663 403 km² (F. obovata Tanaka). The optimum climate region for F. polyandra Tanaka mainly extended to Chongqing, Guangxi, Guangdong, Hainan, and south of Yunnan, while that for the other five species was predominantly distributed in Hunan, Jiangxi, Guangxi, Fujian, Zhejiang, and Guangdong; some favorable region for F. obovata Tanaka even extended to Chongqing. The main climatic factors affecting the growth of Fortunella include minimum temperature, precipitation, and isothermality. The major climatic factors affecting F. hindsii Swingle distribution included isothermality and precipitation in April and June, while for F. margarita Swingle such climatic factors comprised precipitation in April and June, minimum temperature in February and July, and isothermality and precipitation in the driest month. Similarly, geographical distribution of F. japonica Swingle was influenced by precipitation in April and June, minimum temperature in July, isothermality and precipitation in the driest month, and precipitation in the warmest quarter. Likewise, the major climatic factors affecting natural distribution of F. polyandra Tanaka comprised precipitation in July and in December, minimum temperature in February and June, isothermality, and mean precipitation in the warmest quarter. Similar analytical results demonstrated that the dominant climatic factors affecting the distribution of both F. crassifolia Swingle and F. obovata Tanaka were in terms of precipitation in June, and isothermality and mean precipitation of the warmest quarter. The area under the curve (AUC) value of the MaxEnt model for all six species exceeded 0.9 and their actual distribution areas were also integrated, which indicated that the predicted distribution range of this study was highly accurate. Consequently, these results are expected to provide scientific guidance for regional investigation and protection of wild species of Fortunella and promotion of its varieties.