Asian lotus (Nelumbo nucifera Gaertn.) is an aquatic plant with ornamental, cultural, economic, and ecological values. China has abundant germplasm resources of Asian lotus. However, in many areas, the wild Asian lotuses have been destroyed and the germplasms is now facing extinction. In addition, the knowledge of the genetic diversity of the wild Asian lotus in China is poor. To identify and protect the germplasms of Chinese wild Asian lotus, eleven genomic-SSR primers, three EST-SSR primers, and three chloroplast DNA primers were used to investigate the genetic diversity among 69 samples of wild Asian lotus from 25 locations in northern China. The genetic diversity of 27 samples of wild Asian lotus from southern China and other countries, the ancient Asian lotus, Asian lotus cultivars from China, and Asian-American hybrids was also compared. The genetic diversity of the wild Asian lotus from northern China was characterized as medium, and the mean values of observed heterozygosity (H_o) and expected heterozygosity (H_e) were 0.087 and 0.552, respectively. Based on a UPGMA dendrogram and STRUCTURE analysis, the wild Asian lotus samples in northern China were divided into three groups. The wild Asian lotus samples from northern China contained 16 haplotypes. The Nei's genetic distance between the wild Asian lotus samples from the Songhua River basin and the Liao River basin in northeastern China was relatively small, and these germplasms might be relatively primitive compared to those from other regions. This study provides essential information regarding the genetic diversity of the wild Asian lotus resources in northern China, and provides a basis for further analysis of population-level genetic evolution through high-throughput sequencing.