At the Vegetable Research Farm in Geneva, NY, the soils from four long-term systems management blocks were assessed for their soil health status using the 2007 Cornell Soil Health Test. Snap beans were planted in four strips within each block with half of the rows overlapping where beans had been planted in 2006 (2-year beans) and half which had not been previously planted to beans (1-year beans) to relate yield to the observed differences in the soil health status between the blocks. Snap bean yield was significantly higher in the IPM-future block (managed using season-long soil-building crops in addition to cover crops and IPM strategies). Due to the dry conditions during the growing season and frequent cultivation, yields were lowest in the organically managed block. Observed differences in root health as a result of differing soilborne fungal pathogen populations were further explored to determine if there were species composition and/or population density differences between the four management systems. ITS sequence primers were identified for specific soilborne fungal pathogens of interest and the methodologies fine-tuned for the sonication and centrifugation of rhizosphere soil from bean plants harvested from the field. However, the limited total amount of DNA extracted from the soil sampled prohibited the use of real-time PCR to further identify and quantify the soilborne fungal pathogen population in these differing soils. Thus, additional work is needed in order to assess the mechanism(s) involved in the observed differences in root health among the four production systems.