We present the first evidence of biological change in all of the pelagic Laurentian Great Lakes associated with recent climatic warming. We hypothesized that measured changes in lake temperature, and the resulting physical changes to water columns, were affecting diatom communities in the Great Lakes. A paleolimnological analysis of 10 sediment cores collected from deep locations throughout the Great Lakes basin indicates a recent (30–50 yr) reorganization of the diatom community to one characterized by elevated abundances of several species from the group Cyclotella sensu lato, coinciding with rising atmospheric and water temperatures. These Cyclotella increases are a probable mechanistic result of new physical regimes such as changing stratification depths and longer ice-free periods, and possibly water quality shifts. Efforts to understand the mechanisms of these changes are ongoing, but this compositional reorganization in primary producers could have important implications to Great Lakes food webs.