Biological soil crusts (BSCs) are microbial assemblages that play important roles in the areas they inhabit, and can influence aspects such as local nitrogen flux, water infiltration, and plant seedling germination. In a dune environment, BSCs can form close connections with sand particles to stabilize dunes at their surface. Despite their potential critical role within Indiana Dunes State Park, little is known about their diversity, ecology, or interactions with plant communities there. The objective of this study, therefore, was to examine abiotic and biotic factors that influence dune BSCs using High Throughput Sequencing (HTS) to characterize the microbial communities. I hypothesized that specific environmental variables would influence BSC microbial diversity. In this study I sampled every 50 m along a 550 m transect, moving from the Lake Michigan shore inward to the hind-dune environment. At each sampling point soil pH, PAR, UV, and chlorophyll and scytonemin pigments were measured, and plant community cover, richness, and diversity were assessed. Moisture, conductivity, and nutrient content (total N and P) were also measured every 100m. Overall, HTS recovered 1,336,336 bacterial sequences across my 30 samples, and five major phyla were found to dominate the BSC samples, these being Proteobacteria (~21% of all sequences), Acidobacteria (~16%), Actinobacteria (~16%), Bacteriodetes (~17%), and Cyanobacteria (~10%). Linear regression analysis revealed a significant negative correlation between observed Operational Taxonomic Units (OTUs) and soil pH, while Mantel Pearson's Correlation tests suggested that the percent of live plant cover, total nitrogen, soil pH, sample aspect, and distance along the transect away from the shore, were all correlated with microbial community structure. Based on the r values for each of these parameters it was concluded that these factors were positively correlated with the microbial community structure. Future studies will need to be done to further evaluate these factors and their effect of the microbial community structure, particularly pH and nitrogen content.