Over the last decades, the Arctic Ocean has been subject to profound changes due to climate change and the observed environmental effects are amplified compared to other regions in the world. Most striking are the severe decline of Arctic sea ice extent and the projection of a predominantly ice-free Arctic Ocean in summer before the end of this century. Sea ice extent affects primary production of algae in sea ice and the surface ocean and, thus, also influences organic matter export to the deep sea. Changes have been shown to affect various size classes of Arctic communities, including bacteria. Since they play essential roles in carbon and nutrient cycling, bacteria are highly important for the biogeochemical functioning of the Arctic ecosystem. Bacterial communities in the Central Arctic, however, remain understudied, and most available studies are difficult to compare due to differences in environmental conditions at time of the study, focus on different environments or varying sampling locations. In the present study, a first knowledge baseline of the bacterial diversity in the Central Arctic Ocean was created by analysis of samples from sea ice, melt ponds, surface seawater, deep-sea sediments and ice algal aggregates, all obtained during the RV Polarstern expedition IceArc in late summer 2012. A combination of molecular fingerprinting using Automated Ribosomal Intergenic Spacer Analysis (ARISA) and 454 massively parallel tag sequencing of the V4-V6 region of the 16S rRNA gene allowed the identification and description of environment-specific bacterial communities. Bacterial community structure differed significantly between the investigated environments and strong variation in community composition could be detected based on relative sequence abundances. The absence of specific bacterial groups in first-year ice that could be detected in multi-year ice highlights potential effects that the projected loss of this habitat may have on biological diversity and biogeochemical cycling in the sea ice environment. High similarities between bacterial groups detected in melt-pond aggregates and in rapidly deposited aggregates in the deep sea indicated a transport of bacteria by the aggregates. Since the export of these aggregates is likely to increase with ongoing thinning of sea ice, a correspondingly higher number of surface-derived bacterial cells may be exported to the deep sea and potentially induce shifts in benthic bacterial community diversity and functioning. Overall, this study provides essential baseline information on bacterial communities in the Central Arctic Ocean for future comparisons and includes first observations on the role of ice algal aggregates as bacterial transporters from the pelagic to the benthos.