China is one of the native places of yams with abundant representative local varieties. However, the genetic differences between these local varieties remains unclear, thus considerably inhibiting their utilization and development. In this study, 26 phenotypic traits of 112 accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence-related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. A total of 56 variations of 20 quality traits were detected in 112 accessions, and the most diverse phenotypic trait was stem color. Meanwhile, seven principal components were obtained from 26 phenotypic traits, with a cumulative contribution rate of 69.39%, and all the accessions were divided into six groups by clustering the phenotypic traits. Unweighted pair-group method with arithmetic means and principal coordinate analysis based on SSR-SRAP marker data showed that 112 accessions were also divided into six groups, similar to the result of phenotypic traits but with a slight difference among few accessions. Results of genetic structure analysis showed that 112 accessions could be divided into two groups; one group composed of the accessions of D. opposita, the most abundant resource in China, and the other group was a collection of the other accessions. In addition, the analysis of the origin and genetic relationship of yam also indicated that the specie of D. opposita may have originated in China. These results clarified the genetic differences in yam in China, thereby providing a basis for the identification, evaluation, and conservation of yam resource.