Brasenia schreberi J. F. Gmel. of the family Cabombaceae is a perennial aquatic plant under first-level national protection in the wild in China. Its young stems and leaves are used as vegetables. It has been also cultivated in China for about 1800 years for its young stems and leaves as a vegetable, now widely grown in Leibo in Sichuan Province, Lichuan in Hubei Province, Shizhu in Chongqing Municipality, Taihu in Jiangsu Province, and Hangzhou in Zhejiang Province. In order to understand the current status of its wild populations in China, we carried out on-site investigation and collection in Hunan, Jiangxi, Yunnan, and Heilongjiang provinces. The genetic diversity of B. schreberi was then analyzed for six cultivars preserved in the National Germplasm Wuhan Aquatic Vegetable Collection and 27 samples newly collected from six wild populations, with the simplified genome-sequencing technology SLAF-seq. The wild populations of B. schreberi were more diverse than cultivated varieties in many phenotypic traits (such as the color of the rolling leaf, the color of the lower surface of the leaf, the leaf size, and the mucilage thickness). Molecular analysis revealed a rich genetic diversity in B. schreberi (π = 0.3456), with the wild populations (π = 0.3386) higher than the cultivated varieties (π = 0.2916), which is consistent with the phenotypic trait analysis. B. schreberi displayed great genetic differentiation (Fst = 0.2654) among the wild populations, with higher genetic variation within the populations (accounting for 76.99%) than among the populations (accounting for 23.01%), indicating that the within population variation was the main contributing factor. Using high-quality SNP loci, the nearest neighboring method was used to construct the clustering tree, with the total 33 samples divided into two groups. The first group contained two Mangshan populations. The second group included the other four wild populations and all the six cultivars. The samples from two Mangshan populations were mixed with each other, indicating relatively frequent gene exchange between the two groups and very low genetic differentiation. In the other group, wild samples from different populations were well separated, indicating that a certain genetic differentiation existed between those wild populations because of geographical isolation. The PCA and structure analysis all confirmed that the Mangshan samples gather together and were distant from the other samples, indicating an obvious differentiation between the Mangshan populations and the other populations. The genetic differentiation between cultivated varieties and wild populations is small (Fst = 0.0674), indicating a relatively low degree of artificial domestication of the cultivated varieties. This article puts forward some suggestions for the protection of B. schreberi resources in China.