Technical Abstract: Organic farming is a growing field of agriculture that is benign on the environment but there are contradictory reports about the impact of these practices on the soil microbial community, i.e. some studies showed higher microbial diversity in organic farms but others showed no differences in diversity. We assessed the impact of organic and conventional potato farming in Colorado on soil fungal communities using 454 pyrosequencing to obtain the most comprehensive community analysis to date. Organic farms showed more soil fungal diversity than conventional farms, and more species evenness with less dominant fungal species. The effect of organic agriculture was also studied in the center of origin of the potatoes, the Andes of Peru where potatoes have been grown organically for more than 5,000 years, to determine if longer co-evolutionary process might alter the outcome. The soil fungal diversity and evenness in Peru were comparable to those levels present in organic farms in Colorado. Our results suggest that organic agriculture promotes microbial diversity and species evenness and thus has the potential of avoiding pathogenic outbreaks that might have epidemic consequences.