The purpose of this study was to determine the most defensible taxonomic level (species or variety) of the diatom Cymbella janischii and whether it qualifies as a Northwest endemic. C. janischii and C. mexicana belong to a guild of stalked colonial benthic diatoms that have been responsible for aquatic habitat degradation and complaints of nuisance algae in the western U. S. New information on the morphology, ecology, and distribution of C. janischii was compared to corresponding information for Cymbella mexicana. Although it shares some structural features with C. mexicana, C. janischii is easily distinguished under the light microscope by its much larger size, closer striae spacing, and unique central area. Cell measurements expand the upper and lower size ranges for both species. A maximum length of 383 μm and width of 68 μm qualifies C. janischii as the largest freshwater diatom in the Pacific Northwest. Ecologically, C. janischii prefers much larger streams with significantly lower concentrations of dissolved solids. Over 95% of the records for C. janischii are from the Pacific Northwest, where it occurs with C. mexicana in only 3% of the samples in which one or the other species occurs. Common diatom associates of C. janischii include other Northwest endemics. Morphological and ecological separation of the two species renders interbreeding unlikely. These findings qualify C. janischii as a separate and distinct species, and its restricted distribution confirms its status as a Northwest endemic. Habitats supporting C. janischii and other Northwest endemics should be protected.