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We describe effects of a pathogen that spread through a dense, rapidly growing, benthic diatom community during two infection periods (February and mid-April 1991) in Sycamore Creek, Arizona. Infected areas appeared as gray rings within a matrix of healthy diatom growth and spread rapidly, eventually covering all benthic substrata and causing algal sloughing (within 2 wk in February and 1 wk in April). Examination of algal material with transmission electron microscopy revealed the presence of invasive bacteria within diatom cells from infected areas, suggesting a pathogenic bacterium as the most probable cause of this phenomenon. Infected areas supported lower chlorophyll a concentrations and contained higher percentages of diatom cells with fragmented or reduced chloroplasts than uninfected areas. Spread of the pathogen appeared to be linked most strongly with diatom densities. The infection spread most rapidly in April, when cell densities were highest, and decimated all diatom species populations. The February infection was more species-specific in its action, affecting large motile and rosette-forming taxa more strongly than small, adnate diatoms. This latter group likely resided at the base of communities and may have been buffered from pathogen transfer by mucilage and/or detrital particles. Consequently, relative abundance of small, adnate diatom taxa increased in algal communities as a result of the February infection. Pathogen-induced alteration of diatom species composition and abundance should influence primary production in this ecosystem and affect the dynamics of organisms that exploit algae as a resource.