Yield loss of corn following a winter rye cover crop discourages farmers in Iowa from adopting cover crops to manage soil and water quality. The addition of cover crops into the cropping system alters microbial community within the rhizosphere of both winter rye and corn by increasing Pythium species that may cause seedling disease. Pythium is more prevalent in corn seedlings following winter rye. Growth chamber experiments were done to evaluate the susceptibility of corn to seedling disease as a function of corn seedling proximity to winter rye plants. Corn seedlings were planted at three distances, 0 cm, 2-3 cm, and 8-10 cm, from terminated winter rye plants. Root rot severity was assessed at crop development stage V2. Quantitative PCR was used to estimate the abundance of Pythium Clade B and Clade F members present in corn roots. Radicle and seminal root rot severity was greater the closer the seedling was to the winter rye plants (P = 0.01). Moreover, a greater abundance of Pythium Clade B was detected in corn grown within the terminated winter rye compared to corn planted further away (P = 0.01). No effect of distance between corn and winter rye was detected for Pythium clade F. This study will inform management practices for farmers to reduce occasional yield loss of corn following a winter rye cover crop.