Hydrurus foetidus is a major primary producer found in glacier-fed streams, which is now threatened by climate change and glacier disappearance. Although it has been reported since 200 years, little is known about this unicellular alga lying at the basis of the food web, which is able to form long filaments (up to 30 cm) and bloom under oligotrophic conditions. In this study, we sequenced, assembled and annotated the nuclear, chloroplast, and mitochondrial genomes of H. foetidus specimen collected in the Swiss Alps. We obtained a high-quality genome, which is 232 Mb in size with 92.5% Busco completeness, and predicted 28683 coding sequences, among which 70% were annotated. We investigated the nuclear genome functions to determine the principal characteristics of the alga, as well as its gene expression across seasons to identify its adaptive traits to varying environmental conditions. Preliminary results indicate H. foetidus is a mixotrophic microalgae which produces an alginate-based extracellular matrix enabling its distinctive macroscopic colonies formation. Differential gene expression analysis reveals a relatively constant expression of genes, suggesting H. foetidus is found in streams characterised by a set of environmental parameters which have little effect on its activity. Due to glacier loss, glacier-fed streams are now changing towards conditions to which H. foetidus may not be adapted. Therefore, more studies about its ecology would allow to understand its adaptive traits to changing environmental conditions, as well as the effect it might have on its prevalence in glacier-fed streams.