The Chukchi Sea was sampled in August of 2011, a year of near-normal sea ice among recent years, and again in August 2012, a year of all time record low sea ice. We exploited this sampling to test the hypothesis that different sea ice conditions are associated with differences in abundances or species composition of microzooplankton through an examination of tintinnids and radiolarians. From 18 stations in 2011, and 19 stations in 2012, organisms were enumerated in plankton net tow material, and chlorophyll determinations made (total and ≤ 20 µm) from discrete depth samples. We found that the low sea ice conditions of 2012 were associated with higher chlorophyll concentrations (both total and the ≤ 20 µm size fraction), compared to 2011. However, tintinnid ciliates and radiolarians were much lower in concentration, by about an order of magnitude, compared to 2011. In both years the radiolarian assemblage was dominated by Amphiselma setosa. The species composition of the tintinnid ciliates was similar in the two years, but there were distinct differences in the relative abundances of certain species. The 2012, low sea ice assemblage, was dominated by small forms in contrast to 2011, when large species were the most abundant. We present these findings in detail and discuss possible explanations for the apparent differences in the microzooplankton communities associated with distinct sea ice conditions in the Chukchi Sea