ABSTRACT: The ongoing decrease in sea ice thickness and extent is expected to have significant implications for protists in the Arctic Ocean. We analyzed protist community composition and diversity in water and sea ice samples to elucidate the impact of sea ice retreat and sea ice origin. Samples were collected during 2 summer periods with contrasting sea ice concentrations (2011 and 2012). The results are based on a combination of ARISA and sequencing of the 18S rRNA V4 gene region. We show for the first time that the regions of ice floe origin play a fundamental role in structuring the sea ice community. Community structure of pelagic protists correlated significantly with sea ice concentrations, water masses and sampling regions. Both habitats differed in protist diversity and composition between years and were less diverse during the recorded sea ice minimum year 2012. A reduction in protist diversity was especially true for rare sea ice algae in 2012, which suggests that sea ice algae might be more vulnerable to climate change. In the future Arctic, changes in protist diversity can be expected due to sea ice decline and a temporal and spatial shift in sea ice formation.