The soilborne fungus Rosellinia necatrix is the causal agent of white root rot disease on numerous plant species, including apple, which, together with the ability to survive in soil for long periods, makes this pathogen difficult to control. To understand the origins of pathogen infestation, a survey of diseased apple orchards in the northeast of Italy was conducted and 35 isolates of R. necatrix were characterized with intersimple sequence repeat markers. High genetic heterogeneity among the collected isolates suggested multiple preexisting sources of inoculum and not movement of infected soil or plant material from a single source. Greenhouse trials confirmed that, as with some other crops, soil water content and temperature were the main factors influencing infection of apple plants, while organic fertilizers and the incorporation of apple wood residues were less important. The efficacy of Trichoderma atroviride SC1 as a biocontrol agent against R. necatrix greatly depended on the timing of application. It reduced white root rot incidence on apple seedlings only if treatment was applied at least 1 week before planting.