Our study is an example of using genetic markers to select genotypes for enriching the gene pool of declining species in protected areas. We analyzed remnants of black poplars from the Wielkopolska National Park (WNP). This species is a pioneer tree characteristic of riparian habitats. The clone archive has been established in the WNP to protect the gene pool of black poplar in this area. Nevertheless, the number of unique genotypes of black poplar in the WNP is too low. We, therefore, genotyped 128 black poplars from three groups adjacent to the WNP using 18 nuclear microsatellites and species-specific genetic markers to select individuals to enrich the archive. The results showed a generally high level of genetic diversity and low genetic differentiation (F<sub>ST</sub> = 0.0353; R<sub>ST</sub> = 0.0250). It seems that all groups experienced a severe bottleneck in the distant past. Trees from Wiórek appear to be the most suitable choice to enrich the WNP’s clone archive. Differences in the gene pools of rare alleles support the inclusion of at least some individuals from Świątniki. Our approach allowed the identification of a group of trees that was most likely established artificially and, therefore, is not suitable for enriching the WNP’s clone archive. We demonstrated that genetic research should be an integral part of a species’ conservation strategy. This is especially relevant for taxa whose natural populations have been subjected to anthropogenic pressures.
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