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Seed-borne asexual species of Epichloë fungal endophyte have proven to be of critical importance in temperate grasses, particularly those grasses sown in pastures in the USA, New Zealand and Australia. These obligate mutualistic fungal endophytes impart meaningful benefits to the host plant through enhancing the plant’s ability to counter various abiotic and biotic stresses. Although there may be detrimental effects on livestock, selected endophytes have been identified and used in commerce to address animal health and productivity issues, while still providing protection to the host grass from stresses. The use of selected endophytes has been explored for cultivated cereals such as rye and wheat (Triticum spp.), with the goal of reducing usage of fungicides and insecticides, and improving the tolerance of the plant to abiotic stresses. A complicating factor is that fungicides may still be necessary for crop management which in turn could be detrimental to the Epichloë endophyte. While this issue has been studied for pasture and amenity grasses, no similar studies have been performed with endophyte-infected cereals. Fungicide treatments, representing a total of five chemical families, were applied either to seed prior to sowing or to foliage of established crops of rye infected with selected strains of Epichloë bromicola (AR3002) or Epichloë bromicola x amarillans (AR3068). In a field trial, two spring applications of five foliar-applied fungicidal products had no detrimental effect on transmission of endophyte to grain (seed-borne endophyte), but one combination did result in lower viable endophyte in the grain. In a greenhouse trial, three seed-applied fungicidal products had no detrimental effect on transmission of endophyte to seedlings. Similar results have been obtained with ryegrass (Lolium perenne). These initial results are promising in demonstrating that while the Epichloë endophyte will reduce the need for fungicides to control plant pathogens, if there are times when fungicides are needed, then options are available that will not adversely affect the endophyte. In addition to further work on rye, the effect of fungicides on Epichloë-infected wheat requires investigation.