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Apple canker, caused by <i>Neonectria ditissima</i> (Tul. and C. Tul.) Samuels and Rossman, is a major disease of apples (<i>Malus domestica</i>) worldwide. <i>N. ditissima</i> infects through natural and artificial wounds. Infected wood develops canker lesions which girdle branches and main stems causing reduced yield and tree death. <i>N. ditissima</i> is difficult to control; removal of inoculum (cankers) is expensive and therefore seldom practiced, whilst effective chemical products are being banned and no biocontrol products have been found to be effective against <i>N. ditissima</i>. This study used cues from a previous apple endophyte community analysis to isolate and test fungal endophytes belonging to the genus <i>Epicoccum</i> as potential endophytic biocontrol agents. <i>Epicoccum nigrum</i> B14-1, isolated from healthy apple trees, antagonised <i>N. ditissima</i> in vitro and reduced the incidence of <i>N. ditissima</i> infections of leaf scars by 46.6% and pruning wounds by 5.3% in field conditions at leaf fall. Autumn application of B14-1 conidia increased <i>E. nigrum</i> abundance in apple tissues at 10–20 days post-inoculation by ca. 1.5×, but this returned to control levels after one year. <i>E. nigrum</i> B14-1 did not cause detrimental effects on apple foliage, buds, fruit, or growth and could therefore present a new biocontrol agent to manage <i>N. ditissima</i> in commercial apple production.