<>Little is known about factors that determine fungal endophyte community structure.  We use maize as a model system to ask, what is the influence of phytoanticipin production on endophyte communities?  Some maize varieties have been selectively bred to produce high quantities of benzoxazinoids (Bxs), phytoanticipins that are toxic to microbes, insects and plants.  The fungal genus Fusarium contains several species associated with maize that reside as asymptomatic endophytes or pathogens, and can metabolize Bxs.  We conducted in vitro experiments to assess the influence of phytoanticipins on the outcome of fungal-fungal interactions, and found that some endophyte species facilitate other fungi in the presence of Bxs.  We then hypothesized that, i. Bx production increases the ecological fitness of Fusarium in maize, and ii. presence of Fusarium facilitates colonization of additional endophytes. In 2005, non-Bx and high-Bx producing maize varieties were planted in two locations in Ontario, Canada.  Fungal endophyte communities were characterized, and we found that Bx production allows Fusarium to dominate endophyte communities.  Plants that do not produce Bxs harbor a more diverse and even distribution of fungi as compared with Bx-producing plants.  In 2006, non-Bx and high-Bx varieties were planted in Ontario and Georgia (USA).  Seed was treated in two ways prior to planting: i. sterilized or ii. inoculated with Fusarium.  Data indicate that both Bx-production and presence of seed-born Fusarium act as a filter in maize endophyte community assemblage.  The same trait bred to protect maize against pests may select for this species group of economically important pathogens.