To clarify the genetic diversity of Actinidia Lindl. germplasm resources in Yunnan province of China and provide insights for future exploration and protection, this study conducted a field survey and collection in five regions including northeastern, eastern, southeastern, southern, and northwestern. 211 collected wild germplasm resources were subjected for morphology observation and fruit quality quantification (including sugar and acid and VC contents), and genotyped using ten SSR primer pairs. Most of these genotypes were classified belonging to the A. chinensis Planch and the A. deliciosa, and the remaining genotypes were the Jingli Actinidia Lindl, the purple-fruited Actinidia Lindl., and the Gongshan Actinidia Lindl. In Zhaotong city from northeastern Yunnan the abundant and extensive distribution of wild Actinidia Lindl germplasm resources were observed. The analysis on fruit morphological traits revealed a rich phenotypic diversity. The total sugar content of 66 resources ranged from 0.08% to 8.90%, and 57.58% of genotypes showed 0.08%-5% on total sugar content. 45 resources had total acid content ranging from 0.75% to 2.90%, and 71.11% of genotypes showed 1%-2%. The VC content of 61 resources ranged from 4.74-523 mg/100 g, and 78.69% of genotypes showing VC content below 100 mg/100 g, 19.67% of genotypes (VC content between 100-200 mg/100 g), and 1.64% of genotypes showing over 200 mg/100 g were observed. The significant diversity on the total sugar, total acid and VC content were identified in the wild resource collection. Based on the phenotypic datasets, seven elite wild germplasm resources were identified. Moreover, genotyping using 10 pairs of SSR primers produced 421 bands with 100% polymorphism, with an average effective allele number of 1.0772 and the Shannon's information index of 0.1246. These markers were able to classify 211 germplasm materials, implying the rich genetic diversity of Actinidia Lindl. germplasm resources. Collectively, this study provided useful germplasm resources to accelerate the research and utilization of Actinidia Lindl. germplasm resources in Yunnan province of China.