The Actinidia chinensis complex, a group of commercially important fruits (kiwifruit), is a complex of functionally dioecious lianas of variable ploidy. To understand the cytogeography better and to facilitate breeding in this complex, we examined the ploidy and morphological variations in 16 natural populations of A. chinensis var. chinensis and A. chinensis var. deliciosa across an ecogeographical gradient. Four ploidy levels were found, var. chinensis consisting of diploids and tetraploids and var. deliciosa consisting of tetraploids, pentaploids and hexaploids. Hexaploids were centred in the western Yun-Gui plateau, tetraploids coexisted with hexaploids or diploids in the middle Yun-Gui plateau and the Wuling-Xuefeng mountains, and diploids occurred in the eastern Wuling-Xuefeng mountains and the Hunan foothills. These findings indicate a gradual, clinal transition from hexaploid to diploid across the elevational and longitudinal gradient. The clear geographical segregation of diploids and hexaploids may have arisen from their differential ecological adaptation in response to altitude and climate, whereas the coexistence of cytotypes (2x–4x, 4x–6x and 4x–5x–6x) might be a result of reproductive barriers, with a particular contribution from the postzygotic reproductive isolation between ploidy races. The geographical pattern and morphological variation of cytotypes suggest a hybrid zone between the varieties in the Wuling-Xuefeng mountains. The differences in cytotypes which have arisen as a result of ecological adaptation, distribution and morphological characteristics will provide important baseline data for the selection of germplasm and the breeding of kiwifruit.