This study documents, for the first time, the abundance and species composition of protist assemblages in Arctic sea ice during the dark winter period. Lack of knowledge of sea-ice assemblages during the dark period has left questions about the retention and survival of protist species that initiate the ice algal bloom. Sea-ice and surface water samples were collected between December 27, 2007 and January 31, 2008 within the Cape Bathurst flaw lead, Canadian Beaufort Sea. Samples were analyzed for protist identification and counts, chlorophyll (chl) a, and total particulate carbon and nitrogen concentrations. Sea-ice chl a concentrations (max. 0.27 µg/l) and total protist abundances (max. 4 x 10**3 cells/l) were very low, indicating minimal retention of protists in the ice during winter. The diversity of winter ice protists (134 taxa) was comparable to spring ice assemblages. Pennate diatoms dominated the winter protist assemblage numerically (averaging 77% of total protist abundances), with Nitzschia frigida being the most abundant species. Only 56 taxa were identified in surface waters, where dinoflagellates were the dominant group. Our results indicate that differences in the timing of ice formation may have a greater impact on the abundance than structure of protist assemblages present in winter sea ice and at the onset of the spring ice algal bloom.