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Abstract Little is known about biological soil crust (BSC) formation during the early stages of primary succession following glacial retreat. Here, we report on focused sampling of twelve discrete BSC colonies near the snout of a retreating glacier in the High Arctic and show that BSC colonies had significantly higher 16S and 18S rRNA gene diversity than the simpler communities of bare sediments sampled next to each colony. Surprisingly, the colonies also had a higher degree of community dispersion than the more clustered bare sediment controls. There were only eight 16S amplicons that showed 100% prevalence in all 12 of the colonies, and the three most abundant of these keystone amplicons were cyanobacteria, including a nitrogen fixing Nostoc. The only 18S amplicon common to all colonies was a diatom related to Sellaphora. This prominence of phototrophs indicates that early-successional BSC colonies are being supported by photosynthesis rather than ancient- or aeolian-derived organic matter. Co-occurrence network analysis among the phototrophs and fungi identified several potential early-successional soil lichens. Overall, our fine-scaled sampling revealed new insights into community assembly and function in actual communities of interacting microbes (as opposed to mixed communities in bulk soil samples) during the early stages of primary succession.