High throughput V3-16S rRNA amplicon sequencing data was used for evaluating differences between free-living (FL, <1.2-0.2 μm) and particle-associated (PA, >1.2 μm) bacterial communities, and their spatial variation between inner fjord (IF) and outer fjord (OF) of Kongsfjorden. A total of 4,454,142 high quality sequences obtained clustered into 32,058 OTUs. A majority of these sequences were affiliated with Proteobacteria (59.8%), followed by Bacteroidetes (29.02%), Firmicutes (5.9%), Actinobacteria (2.84%), Cyanobacteria (1.04%), and others (1.4%). The highest bacterial diversity was recorded in the inner fjord free-living (IF_FL) fraction whilst the lowest was observed in the outer fjord free-living (OF_FL) fraction. There was a clear spatial variation among FL bacterial communities, while PA communities remained similar at both sampling locations. The free-living bacterial community differs from particle-associated community and had relatively higher abundance (>4-fold) of Alteromonas and Pseudoalteromonas, while PA community was relatively more enriched with Balneatrix, Ulvibacter, Formosa, Candidatus Planktomarina, Sulfitobacter, Loktanella, members of SAR116, and Acidimicrobiales. In addition, two major bacterial taxa, Polaribacter and SAR11, co-occurred in both FL and PA fractions with varied proportions in IF and OF. These results suggest co-occurrence of PA specialist as well as generalist bacterial groups in Kongsfjorden. Further, high bacterial diversity in the IF_FL fraction indicates possible role of glacial inputs in modulating diversity of free-living bacterial community in Kongsfjorden.