Better understanding factors that have a direct response on soybean yield has led farmers in Iowa to plant earlier in the spring, when conditions are still cool and wet. Implementation of these practices also leads to a shift on the range of pathogens that infect soybeans in the seedling phase. We hypothesize earlier plating dates of soybean will favor pathogens that prefer damp and cool conditions like Pythium spp. over Phythopthora spp, that develops at higher temperatures. The objective was to determine the incidence of specific soil-borne pathogens in a fumigated vs. non-fumigated soil using early planting practices for optimum productivity. Incidence of Phytphthora spp, Pythium spp., and Rhizoctonia spp. in soybean seedlings was assessed for 6 varieties at two locations in central Iowa (Whiting and Nevada), where part of a field was fumigated with a mixture of 1-3-dichloropropene and chloropicrin (Telone C-35 ™). The varieties were sampled 21 days after emergence, and incidence of the three pathogens was determined by using ELISA kits (Neogen Corporation, Lansing, Miami, USA; Agdia, Elkhart, Indiana, USA). Incidence of the three pathogens was lowered in the fumigated fields, when compared with the control, although this difference was significant for Pythium spp. Differences among varieties were not significant, except in the fumigated low-yielding environment (Nevada). In this location, Pythium spp. inoculum was reduced enough to show differences in incidence of 60% in the same variety when compared with the control. Overall, Pythium was the most common pathogen detected in the roots, followed by Rhizoctonia and Phytophthora. This information is important because farmers still consider Phytophthora as the main cause of stand reduction and damping off early in the season.