In order to understand the genetic diversity of kiwifruits in southwest of China, AFLP system for kiwifruits was optimized. The optimum AFLP system was constructed as following: 300 ng DNA was digested with EcoR I/Mse I (15 U/5 U) at 37℃ for 2 h, diluted by 5-fold after ligating with adaptors for the preamplification, and then the production of pre-amplification diluted 10-fold was used for selective amplification. The results showed that 979 electrophoretic bands were identified totally, of which 649 bands were polymorphic by using 22 pairs of primers. The genetic diversity of ten kiwifruit species, including Actinidia chinensis, A. deliciosa, A. chinensis var. hispida, A. venosa fo. pudescens, A. rubricaulis var. coriacea, A. tetramera, A. kolomikta, A. ploygama, A. callosa var. henryi and A. arguta var. purpurea, from southwestern China, were analysis by using the optimum AFLP system. The results indicated that there were obvious clustering relationship among intraspecific and interspecific, and cross cluster existed in species between sect. Maculatae and sect. Leiocarpae, related to geographic regional distribution.