The aim of the paper was to test the hypotheses on the genetic structure and origins of forest herbaceous plant species, Galium schultesii and Stellaria holostea, in the subalpine zone of the Bieszczady Mts. The species are generally the lowland elements occurred in fertile oak-hornbeam forests. Their extrazonal occurrence in the mountain subalpine zone could be an effect of recent, Holocene migrations from various glacial refugia or the surviving in situ the last glacial maximum (LGM) in cryptic forest refugia. The two hypotheses were tested with the use of AFLP genetic fingerprinting and the patterns of bands distribution were established based on General Linear Models (GLMs) and STRUCTURE analysis. Twenty nine populations of G. schultesii and thirty five population of S. holostea were sampled in the Carpathians, Transcarpathia, Pannonian Basin, Transilvania and Podolia. They were characterized by 200 and 219 AFLP loci, respectively. The Bieszczady’s populations of both species, as a geographical group, were not divergent from the adjoining regions (Analysis of Molecular Variance AMOVA, p > 0.05). In G. schultesii a group of AFLP bands in three populations from the Bieszczady Mts. were found in Transcarpathia and the Piatra Craiului Mts (E Carpathians). In S. holostea a group of AFLP bands were found in four of the Bieszczady’s populations, in the Eastern Romanian Carpathians (the Maramaros and Kelemen Mts.), and the Sandomierz Basin (Niepołomice Forest, north of W Carpathians). Both groups could have reflected a refugial pattern. The putative refugial vs. non-refugial groups had statistically significant between group variation (AMOVA) for both G. shultesii (4,8%, p = 0.006) and S. holostea (11,2%, p < 0.001). Statistical analysis showed that putative refugial group of S. holostea had statistically significantly lower indices of genetic richness FA (p = 0.03) and FAmax (p = 0.01), and higher divergence DW index (p = 0.002), in comparison to the non-refugial group. It could be an effect of the genetic bottleneck. Galium schultesii had significantly higher indices of genetic diversity: PPL (p = 0.008), Nei’s h (p = 0.037), Shannon I (p < 0.001), and divergence DW index (p = 0.007) in the putative refugial group. Probably both forest herbs could have persisted the LGM in the Bieszczady Mts.