Abstract Pinus sylvestris (Scots pine) and taxa from the P. mugo (mountain pine) complex hybridize in contact zones producing morphologically-intermediate fertile hybrids. However, the hybrid specimens sometimes express only the P. sylvestris phenotype. Such cryptic hybrids were detected among P. sylvestris and P. uliginosa in the western part of Błędne Skały in the Stołowe Mountains, where the pines grow on the tops of sandstone rocks and phenotypically resemble P. sylvestris , P. uliginosa , and P. mugo . Hybrids with the P. sylvestris phenotype could be potentially present in other relic populations of this species in these mountains. During the present study, the hybrids were identified only in the area of Błędne Skały based on chloroplast and mitochondrial markers, morphological differentiation of various needle and cone traits, and phenotype assessments of the trees during sampling. These hybrids included three cryptic hybrids of P. sylvestris × P. mugo with the P. sylvestris phenotype and one displaying the phenotype of P. uliginosa . The other populations analyzed represented Scots pine with no evidence of hybridization with P. uliginosa and/or P. mugo . Biometric data on the cone and needle morphology also suggest possible hybridization within the P. mugo complex on Błędne Skały. The results indicate that hybridization takes place in this population but not in neighboring populations despite the possible connection by pollen-mediated gene flow.