The Greater Yellowstone Area ecosystem experienced major wildfires in 1988, resulting in a substantial number of catchments being burned. We studied diatom assemblage structure at 14 sites over 5 years in catchments ranging from 0 to over 90% burned. Coefficients of variation for selected physical measures provided a good assessment of the degree of disturbance experienced by the various sites and correlated highly with percentage of catchment burned. Principal components analysis quantitatively estimated the degree of temporal change in diatom assemblages at a site. The more extensively burned catchments showed the greatest amount of structural change in diatom taxa among years. Navicula permitis Hust. and Nitzschia inconspicua Grun. were predominant in the heavily disturbed systems, whereas Achnanthes minutissima Kuetz., A. lanceolata (Breb.) Grun., Rhoicosphenia curvata (Kuetz.) Grun. ex Rabh., and Diatoma hiemale var. mesodon (Ehr.) Grun. were common in less disturbed streams. The results demonstrate that recovery trajectories of lotic diatom assemblages following major landscape-scale disturbances are a function of disturbance intensity resulting from differences in catchment characteristics.