This study examined the abundance, cell size, and activity of Bacteria and Archaea in the Chukchi Sea and the Canada Basin of the western Arctic Ocean in the spring (May-June) and summer (July-August) of 2002 and 2004. Data from fluorescence in situ hybridization (FISH) analyses indicate that bacterial abundance as a percent of total prokaryotes decreased with depth, whereas in contrast, Crenarchaeota increased from about 10% of prokaryotes in surface waters to as much as 40% in samples from 100 to 200 m. Euryarchaeota were detectable in only a few samples. Relative abundance of Crenarchaeota, expressed as a percent of total prokaryotes, correlated with ammonium concentrations, but relative bacterial abundance did not. Crenarchaeota cells were significantly larger than Bacteria by 1.5- to 2-fold in the upper 200 m. Data collected from a combination of FISH and microautoradiography indicate that often the fraction of both Bacteria and Crenarchaeota assimilating organic compounds was high (up to 55%), and both microbial groups were more active in assimilating amino acids than other compounds. However, Crenarchaeota were usually less active than Bacteria in assimilating amino acids and glucose, but were nearly as active as Bacteria in assimilating protein and diatom extracellular polymers. The fraction of Bacteria and Crenarchaeota assimilating CO2 in surface waters was higher than expected by anaplerotic fixation alone, suggesting that many of these microbes are chemoautotrophic. These data add to a growing body of evidence indicating how the roles of Archaea and Bacteria differ in biogeochemical cycles of the oceans.