Black poplar (Populus nigra L.) is one of the main woody riparian species in Europe. Because of extensive habitat loss due to river regulations, this species is considered rare and threatened. To analyze genetic diversity and spatial genetic structure, we examined ten nuclear microsatellite loci in a population of very old P. nigra trees growing along the Vistula River in Poland. We found a high level of genetic diversity (H E = 0.792, H O = 0.731, A = 14.7) that was within the range of other natural European P. nigra populations, and our results showed that sexual propagation is the dominant way of reproduction in the studied population, leading to high clonal diversity (R = 0.91). Additionally, we did not detect a spatial genetic structure resulting in a random spatial distribution of genotypes. Individuals from such old and diverse populations have the potential to provide valuable reproductive material for both restoration programs and breeding purposes.