Soybean cyst nematode (SCN) is one of the most important pathogens of soybean. Our hypothesis is that organic production systems impact SCN and other nematode populations. Soil samples were collected from four organically certified soybean fields with long or short-term rotations in central Illinois. Cysts were detected in three of four fields. To determine if these soils were suppressive to SCN, an SCN susceptible soybean cultivar was planted into pots containing these four field soils and infested with SCN eggs. After 35 days, soils from the two fields with long term rotations (5-7 years) had 47 and 39% lower cyst counts, respectively, than the control. Soils from the fields with shorter rotations (3 years) had 0 and 38% higher cyst counts, respectively, than the control. To examine if the nematode community impacts SCN, vermiform nematodes were extracted from the original soil samples. The most abundant plant parasitic nematode was Hoplolaimus sp. followed by Pratylenchus sp., Meloidogyne sp., and Xiphinema sp.. Indices for soil health indicated the soil communities were enriched but less structured suggesting that nematode communities in these systems are characterized by families of opportunistic life history characteristics. Less suppressive soil was shown to be more structured than more suppressive soil indicating that the natural suppressiveness might be associated with other members of the soil food web.