This study presents the first integrated analysis of cyanobacterial and microalgal diversity in soils and biological soil crusts from the sand dunes of the Russian High North, combining morphological characterization with DNA barcoding of cultured isolates. We identified 33 taxa across four phyla, dominated by Chlorophyta (Trebouxiophyceae and Chlorophyceae). Although ITS2 sequencing is widely used for phylogenetic studies, only approximately 35% of eukaryotic algal strains in our study could be confidently identified to the species level, underscoring both the limitations of this marker for certain taxonomic groups and the ongoing challenges in algal systematics. ITS2 sequencing limitations as a single-locus marker were revealed when analyzing phylogenetically complex genera, including Asterochloris, Klebsormidium, Interfilum, and Vischeria, where robust classification required integration of additional genetic markers. Phylogenies revealed taxonomic gaps in several algal lineages (Spongiococcum, Myrmecia, Leptosira, and the Radiococcaceae family), exacerbated by critical gaps in reference databases. We identified eight novel candidates via concordant molecular and morphological divergence, including one potential new genus. Ecological roles varied, ranging from free-living soil crust formers (Klebsormidium spp., Kalymmatonema sp.) to lichen symbionts (Asterochloris spp., Myrmecia israelensis). Remarkably, we documented the rare cyanobacterium Dapisostemon apicaliramis in these sand dunes, expanding its known range beyond Brazil. Our findings demonstrate the necessity of multi-locus approaches to resolve taxonomic uncertainties in understudied genera, while emphasizing the crucial role these microbial communities play in stabilizing fragile northern taiga ecosystems in Western Siberia. Keywords: Soil · Biological soil crusts · Lichen · Cultivated biodiversity · 16S rRNA · ITS2.