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As a complex ecosystem, the soil maintains both beneficial and pathogenic microorganisms that coexist in balance with their hosts. When the conditions are conducive, soilborne pathogens proliferate, causing damage and impacting the quality and yield of crop plant species. The most common oomycetes and fungi associated with soilborne diseases belong to the genera Pythium, Phytophthora, Fusarium, and Rhizoctonia. However, some conditions can favor the growth of non-traditional pathogens, promoting the emergence of new diseases. Our research focuses on the ecology and the effects of Pythium and Phytophthora spp on soybean and corn over the growing season. Using amplicon approaches, we monitored oomycete communities at different host growing stages to determine the pathogen prevalence and its impact on the host. While oomycete communities on corn were stable throughout the season, our analyses detected an increasing diversity due to a change in composition on soybean communities. In addition, we are also investigating the emergence of a new disease named taproot decline caused by fungi belonging to the genus Xylaria, in the group arbuscula. By understanding the ecology of soilborne pathogens we can tailor management practices to control their impact and minimize economical losses.