Aim of study: We performed a fine scale characterization of two European black poplar (Populus nigra) in situ conservation units, using a large sample of individuals and a comprehensive set of genetic markers. This information is pivotal to understand the population dynamics of the units for implementing conservation and management plans. Area of study: We studied two populations with distinct environments and management practices in Spain and Austria. Material and methods: We genotyped 500 adults and 250 juveniles within each population using 13K single nucleotide polymorphism (SNP) markers. The populations were characterized in terms of fine scale genetic structure and clonality, while controlling for genotyping errors. Main results: The genomic data, with a low error rate, allowed the identification of groups of clones. The proportion of clonal individuals was 21.7% in Austria and 12.9% in Spain, despite efforts to avoid sampling obvious clonal copies. Some ramets within clonal groups were found more than 60 m apart at both sites. The genetic population structure of black poplar is complex in the two investigated sites, resulting from both clonal and sexual relationships among the individuals. Research highlights: A large number of SNP markers reveals novel information about within-population relationships in black poplar. We found substantial clonal reproduction, together with a high number of distinct genotypes resulting from sexual reproduction and/or migration. This structure allows natural selection to operate at two levels. We should take into consideration this complex genetic structure in conservation management to preserve the adaptive potential of the species under future climate conditions.