Abstract Gene flow among individual trees of Pinus sylvestris and P. mugo putative hybrid swarms in Slovakia was fol-lowed at four localities using the species-diagnostic cpDNA trnV-trnH/Hinf I restriction profile. Variable proportions of P. sylvestris and P. mugo haplotypes were revealed among the sampled localities. Low between-habitus consistency of the trees and their cpDNA haplotypes indicates the hybrid nature of the swarms. Molecular analy-sis based on mutual comparison of the haplotypes of a given tree and its embryos suggests direct and recipro-cal hybridization between trees of the P. sylvestris and P. mugo haplotypes. Besides conspecific embryos resulting from hybridization of trees with the same haplotype (P. sylvestris × P. sylvestris and P. mugo × P. mugo), hybrid embryos of P. sylvestris × P. mugo (8.03%) and P. mugo × P. sylvestris (11.50%) were also detected in open-pollinated offspring. The results are discussed from the standpoint of primary and introgressive hybridization between the parental species.