<p>The <i>Pinus mugo</i> complex (<i>P. mugo</i> Turra s. l. or <i>P. mugo</i> aggregate) is an important fragment of European dendroflora, which is characterized by high variability, reticulate evolution, and several hybrid zone populations in different parts of Europe. Here we tried to explore the admixture structure of four putative hybrid zones between <i>P. mugo</i> Turra (s. str.) and <i>P. sylvestris</i> L. in Slovakia, using Bayesian ancestry inference with microsatellites. Unexpectedly, compared to nine reference populations, the results showed no elevated allelic diversity in our four locations. However, there was a high marker information content for ancestry based on the reference samples (<i>δ</i>_<i>C</i> or <i>D</i>_<i>K</i> = 0.451). The individual admixture proportions of <i>P. sylvestris</i> averaged at 0.529, 0.419, and 0.292 in the three locations, with the distribution ranging from unimodality to bimodality. These data support the presence of hybrid zones, but only in association with peatland habitats. In a typical calcicolous pine relict examined, no hybrids were detected, which contrasts earlier reports. The unexpected absence of elevated diversity, including the differences in hybrid zones’ modality within the same habitat, might be explained by population bottlenecks due to anthropogenic peatland degradation during the 1960s to 1980s, when intensive drainage in the region occurred. The study highlights the evolutionary, ecological and conservation value of the studied bog populations.</p>