The centric diatom Stephanodiscus yellowstonensis Theriot and Stoermer is endemic to Yellowstone Lake, where it can be an important component of the summer phytoplankton assemblage. Its close relative, Stephanodiscus niagarae Ehrenberg, is abundant in nearby lakes and regional reservoirs. We used the stratigraphic record of Yellowstone Lake to investigate the evolution of S. niagarae to S. yellowstonensis and to describe the limnologic and climatic conditions associated with its evolution. A dramatic morphological shift took place between about 13.7 and 10.0 Ka, but morphology remained stable from 10 Ka to the present. Coincident with morphological change in the S. niagarae/S. yellowstonensis complex were changes in the diatom species assemblage, biogenic silica concentrations, sediment lithology, and regional vegetation. These changes suggest an environment that experienced progressive warming following the retreat of continental glaciers. We could not identify a specific selective factor driving evolution. Nevertheless, nonrandom morphological evolution strongly associated with continuous environmental change suggests that directional selection is a reasonable hypothesis to account for evolution of S. yellowstonensis. Protists are presumed to evolve gradually after speciation events because of large population size, high dispersal capacity, and low reproductive barriers. However, published diatom examples and the evolution of S. yellowstonensis suggest that it is premature to generalize about rates of evolution in protists, or at least to include diatoms in this generalization.