The Hudson Bay is an iconic cryo-environment that marks the ecological transition between Canadian Subarctic and Arctic biomes. Although the Hudson Bay has been subjected to various ecological monitoring programs in the past, knowledge of prokaryotic communities in this dynamic ecosystem is scarce. This study aimed to assess the structure of winter prokaryotic communities at the interface between surface ice and the underlying water along a natural salinity gradient at the Hudson Bay coast. We used high-throughput, Illumina sequencing of 16S rRNA genes to describe the prokaryotic communities at the Hudson Bay.