Summary High latitude and altitude freshwater systems are highly sensitive to the effects of global warming and associated environmental changes. Diatoms are widely used as sentinels of environmental change, yet knowledge of diatom community patterns in high latitude and altitude streams remains limited. The aim of this study was to examine alpha and beta diversity of diatoms in subarctic streams in Finland and Norway, and to determine the importance of local environmental factors and elevation in shaping their community patterns. We also aimed at testing, for the first time, whether microbes conform to Rapoport's elevational rule, which states that species occurring at higher elevations have generally larger elevational ranges than species at lower elevations. Three streams (44 sites in total) with an altitudinal gradient of 21–877 m a.s.l. were sampled. Generalized linear models, hierarchical partitioning, and a boosted regression tree method were used to identify drivers of diatom species richness. We ran Mantel tests, and calculated initial similarities and elevational halving distances to examine beta diversity. There were no apparent richness–elevation relationships within streams. Across all study streams, the water depth was the most important factor for richness, with additional influences by stone size, conductivity, pH and elevation. Diatoms in subarctic streams did not conform to Rapoport's elevational rule. Community similarity decreased significantly with elevational distance while distance decay was weaker with environmental distance. Our results suggest that diatom alpha and beta diversity along stream elevational gradients are shaped by interacting local environmental factors such as water depth and substrate size, indicating vulnerability of diatoms to physical disturbances, and regional factors such as dispersal and geographical variables. Diatom diversity patterns do not seem to concur with patterns often observed for larger organisms as no consistent elevational patterns in richness or range sizes were found.