Approximately 0.5 million km of tropical stream channel are modified by catchment deforestation annually, but the consequences of this process for community structure are poorly understood because of a dearth of data from tropical regions. We compared the algal communities of epilithic biofilms from 3 tropical rainforest streams draining Ranomafana National Park (RNP) in eastern Madagascar and 3 open-canopy streams draining RNP's deforested peripheral zone. Forest and open-canopy streams differed in canopy cover and mean water temperature but did not differ in substrate composition or major nutrient chemistry. We recorded 137 algal taxa, of which ∼45% can be considered endemic or potentially endemic. Deforestation had significant effects on algal community structure. Complete separation between forest and open-canopy streams was observed in nonmetric multidimensional scaling ordinations based on species cell densities, species presence–absence, and cell densities of algal growth forms. Forest streams were characterized by higher species richness and cell densities of motile and solitary growth forms (e.g., Navicula spp.) than were open canopy streams. Open-canopy streams had more variable community structure than forest streams and were characterized by prostrate and solitary (e.g., Planothidium spp.) and chain-forming/stalked growth forms (e.g., Gomphonema spp.). Community shifts and reductions in species richness observed in open-canopy streams show that diatom biodiversity might be affected adversely by vegetation removal in the catchments we studied. Given that Madagascar has lost most of its rainforest in recent centuries, it is reasonable to assume that historical deforestation has led to shifts in algal assemblages at broader regional scales. Our results also suggest that global algal diversity could be affected by tropical deforestation if similar patterns of endemism and alteration of algal assemblages occur in the 0.5 million km of stream channel affected by tropical deforestation annually.