Vaccinium myrtillus L., V. vitis-idaea L. and V. uliginosum L. belong to the genus Vaccinium. These wild species are widely distributed and ecologically important within the Baltic countries but they have not been extensively studied using molecular markers. EST-SSR and cpSSR markers were used to investigate the population structure and genetic diversity of these species to obtain information useful for the development of in situ conservation strategies. Wild Vaccinium species populations are moderately genetically differentiated, with some populations more highly differentiated, but without higher order clustering of groups of populations, indicating that there are no dispersal barriers for these species within the Baltic countries. Genetic diversity of populations growing in protected areas, managed forests and intensively utilised public recreational areas is similar. The results from this study can be utilised for the selection of populations for the in situ conservation of the studied Vaccinium species. In addition, complementary ex situ conservation strategies can be used for the preservation of rare varieties (e.g. V. myrtillus var. leucocarpum).