The southwest Yukon Territory, Canada, is an important region for recovering sensitive records of Holocene paleoclimatic change. More information is needed, however, to constrain the timing of the major Holocene climatic transitions, and to understand associated impacts on different ecosystems. For example, paleolimnological studies have focused on small lakes and ponds, but the history of large lakes has received little study. We analyzed diatom assemblages, species richness, valve concentrations, and biogenic silica, in the sediments of Kusawa Lake (60°16.5'N; 136°10.9'W; 671 m a.s.l.) to reconstruct the responses of this large (surface area = 142 km2), deep (Z
max = 135 m) freshwater ecosystem to Holocene climatic transitions. Diatoms colonized the lake soon after ice retreat, around 11,000 cal yr BP; assemblages throughout the record were dominated by planktonic types. Diatom concentrations and biogenic silica were high during the Holocene Thermal Maximum between 10,700 and 7300 cal yr BP, then began to decrease in response to cooling associated with orbitally driven reductions in insolation. Diatom assemblages shifted towards taxa with lower surface water temperature optima after 8300 cal yr BP, perhaps in response to abrupt and progressive cooling. Our study confirms that diatom assemblages in large lakes are sensitive to regional-scale paleoclimatic changes.