The wild sacred lotusNelumbo nuciferais considered as an endangered aquatic plant in China and Russia. To date, the assessments and comparisons of the genetic diversity of wild populations ofN.nuciferain Russia and China are very limited. Here, we sampled 15 wild populations ofN.nucifera,including 208 individuals from these two key areas and genotyped using 13 microsatellite markers. Our results revealed 154 multilocus genotypes (MLGs) among individuals. Excluding the NS049 Locus that showed significant null alleles, we further assessed the genetic diversity of 154 MLGs in our study. The Chinese populations exhibited slightly lower genetic diversity compared to the Russian ones. Overall, the study showed low levels of genetic diversity (H-O = 0.174 andH(E) = 0.251) with substantial genetic differentiation (F-ST = 0.547) inN.nuciferapopulations. We found a greater genetic variation residing among populations (54.74%) and a significant correlation (R-2 = 0.8756,P = 0.01) between genetic and geographic distances. In Bayesian analyses, we found that the populations were clustered into three distinct genetic pools (K = 3) supported by principal coordinates analysis (PCoA) and neighbor-joining (NJ) tree. We observed low gene flow between the genetic pools (N-M = 0.2649). Nine of the 15 populations showed recent bottlenecks, demonstrating theN.nuciferapopulations were vulnerable or endangered in Russia and China. Therefore, based on the available genetic variations and the levels of threats, we recommended important population sites for the preservation ofN.nuciferathrough complimentary conservation approaches.