Endophytic bacteria inhabit internal plant tissues, and have been isolated from a large diversity of plants, where they form nonpathogenic relationships with their hosts. This study combines molecular and culture-dependent approaches to characterize endophytic bacterial communities of three arcto-alpine plant species (Oxyria digyna, Diapensia lapponica and Juncus trifidus) sampled in the low Arctic (69°03′N). Analyses of a 325 bacterial endophyte isolates, as well as seven clone libraries, revealed a high diversity. In particular, members of the Actinobacteria, Bacteroidetes, Firmicutes, Acidobacteria, and Proteobacteria were found. The compositions of the endophytic bacterial communities were dependent on host-plant species as well as on snow cover at sampling sites. Several bacterial genera were found to be associated tightly with specific host-plant species. In particular, Sphingomonas spp. were characteristic for D. lapponica and O. digyna, and their phylogenetic grouping corresponded to the host plant. Most of the endophyte isolates grew well and retained activity at +4 °C, and isolate as well as clone library sequences were often highly similar to sequences from bacteria from cold environments. Taken together, this study shows that arctic plants harbour a diverse community of bacterial endophytes, a portion of which seems to be tightly associated with specific plant species.