The SCIN (Soil Crust International) project is a multidisciplinary research initiative that aims to achieve improved understanding of the BSCs of Europe, one facet being an investigation into the cyanobacterial communities of BSCs across a latitudinal gradient. Cyanobacteria community assemblages were analysed by both morphological and molecular analysis. Two treatments were applied prior to DNA extraction, continued sample wetting and a dry sample process, 16S ribosomal RNA (rRNA) amplicons were processed by Illumina MiSeq sequencing. The results suggest high and variable cyanobacterial diversity with each site having a unique assemblage.