Trees and shrubs belonging to the Betula L. genus present highly confusing interspecific relationships. The complex evolutionary history of birches may be due to several factors: interspecific gene flow, the independent occurrence of both polyploidy and dwarf forms in different lineages, incidents of major speciation events within a very short time period and different selection pressures in the distant populations of widespread species. We assessed phylogenetic relationships between the uncommon dark-barked B. obscura and B. pendula var. carelica with patterned wood texture and widespread birch tree species: white-barked B. pendula and B. pubescens as well as dark-barked B. nigra and B. dahurica, using the internal transcribed spacer ITS1 and ITS2 regions of nuclear ribosomal DNA, nuclear ADH (alcohol dehydrogenase) gene sequences and AFLPs (amplified fragment length polymorphisms). In the phylogenetic trees based on the ITS and ADH gene sequences, B. pendula var. carelica and B. obscura clustered with B. pendula, but were distinct from B. pubescens, B. nigra and B. dahurica. In turn, both clustering and multivariate ordination methods using the AFLPs revealed clear distinctness of B. obscura from the remaining species. Betula pendula var. carelica grouped with B. pendula and B. pubescens individuals in both AFLP analyses. Values of the leaf morphology indices of B. obscura and B. pendula var. carelica were within the range of B. pendula variation. All genetic and morphological analyses confirmed the intraspecific status of B. pendula var. carelica. We also suggest that B. obscura represent intraspecific variation of B. pendula, although discrepancies between nuclear sequences and AFLP results were noted.