The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.