Over the past century, dust emissions have increased in frequency and intensity due to anthropogenic influences and extended droughts. Dust transports microbes, nutrients, heavy metals and other materials that may then change the biogeochemistry of the receiving environments. The purpose of this study was to find whether unique bacterial communities may provide distinct fingerprints of dust sources in the Western USA. We collaborated with the National Wind Erosion Research Network (NWERN) to identify bacterial core communities (core) of dust from ten NWERN sites, and compared communities to location, soil, and regional characteristics. In order of importance, precipitation levels (F = 43, P = 0.0001, Df = 2, r2 = 0.25), location (F = 16, P = 0.0001, Df = 5, r2 = 0.23), soil texture (F = 14, P = 0.0001, Df = 3, r2 =0.12), seasonality (F = 11, P = 0.0001, Df = 2, r2 = 0.064), and elevation (F = 5.7, P = 0.0002, r2 = 0.033) determined bacterial community composition. Bacterial core communities were defined as taxa present in at least 50% of samples at each site and offered predictable patterns of dust communities in terms of abundant (> 1% relative abundance) and rare (< 1% relative abundance) signatures. We found distinct bacterial core communities that reflected dust source systems, for example, sites contaminated with heavy metals contained Romboutsia, Turicibacter, Clostridium sensu stricto 1, Geodermatophilus, and Microvirga. Sites with association to plants and biocrusts contained Methylobacterium-Methylorubrum, Bradyrhizobium, Paenibacillus thermoaerophilus, Cohnella, and bacterial families Solirubrobacteraceae, Sphingobacteraceae, and Myxococcaceae. The presence of Sphingomonas, Stenotrophomonas, Rhodococcus, and Phenylobacterium were found in hydrocarbon contaminated soils. High stress (UV radiation and desiccation) sites contained Deinococcus, Blastococcus, and Modestobacter. We found that seasonal changes affected microbial community composition in five NWERN sites (CPER, HAFB, Jornada, Red Hills, and Twin Valley) (p < 0.05), while no seasonal effects on bacterial distribution were observed at Moab. Our results identify that the use of core microbiomes may offer a fingerprinting method to identify dust source regions.