Glaciers and ice sheets are particularly threatened by the loss of biodiversity due to the widespread melting induced by climate warming. Assessment of the biodiversity in these endangered ecosystems is timely and critical. However, few studies have characterized the algal communities in alpine supraglacial environments, despite their importance for surface albedo, carbon cycle, and global biodiversity patterns. Here, we present the first study of algal biodiversity at a high precision level in the Forni Glacier (Lombardy, Italy) based on microscopic observations of terrestrial and aquatic supraglacial habitats. We identified different supraglacial habitats on the glacier surface, characterized by “terrestrial” substrates (dirt cones, cryoconite sediment, sparse cryoconite) and “aquatic” substrates (bedieres, snow, bare ice, water of cryoconite holes). Biovolume, diversity, and community composition have been assessed at the beginning (July) and the end (August-September) of the ablation season for two consecutive years (2023 and 2024). Our results revealed that the algal biovolume, diversity, and community composition varied spatially and temporally in the Forni Glacier. More specifically, we demonstrated that each supraglacial habitat hosts a distinct community, highlighting the significance of microlocal factors in shaping algal assemblages. By expanding our knowledge of glacier biodiversity, this study constitutes a significant step in forecasting the incidence of algal blooms and anticipating the effects of biodiversity loss in alpine glaciers.