Organic farming is frequently touted as being beneficial to soil health by increasing microbial community diversity; however, contradictory results exist in the literature. In this study, we compared several organic and conventional potato farms in Colorado for differences in soil nutrients and microbial communities using 454 pyrosequencing of the 18S ribosomal RNA gene. Organic farms showed a slightly higher diversity and evenness within the microbial community compared with conventional farms. No difference in the number of observed or estimated total operational taxonomic units (OTUs) was observed between management strategies. However, the relative abundance of 16 OTUs (3% genetic distance) differed between the organic and conventional farms, with seven increasing and nine decreasing in organic farms. A variety of known potato fungal pathogens (e.g., Alternaria spp., Ulocladium spp., and Pythium ultimum) were detected in the soil, including three different OTUs (3% genetic distance) with a high homology to the early blight pathogen Alternaria solani. Relative abundance for Alternaria spp. was higher in conventional farms (relative abundance 30.15 versus 7.8%), whereas the relative abundance for P. ultimum was higher in organic farms (relative abundance 0.25 versus 0.05%). Quantitative polymerase chain reaction, using primers specific for A. solani, Phoma foveata, and Pythium ultimum, yielded similar results to the pyrosequencing, validating the use of pyrosequencing data for the quantification of OTU relative abundances.