A collection of Bacillus and Trichoderma isolates from Iran was investigated for the biological control of pear white root rot caused by Rosellinia necatrix. Among the isolates, B. amyloliquefaciens AP4, B. siamensis AP8 and T. harzianum T20a were selected based on their growth inhibition of R. necatrix in dual cultures, as well as by volatiles, diffusible extracts and culture filtrates. Four pear rootstocks (Pyrodwarf, OHF40, OHF60 and Williams) were assessed for white rot in the greenhouse following soil amendment with the three isolates. For OHF40 rootstock, none of the three isolates significantly reduced disease severity, whereas all three isolates significantly reduced disease severity for OHF69 rootstock. For Pyrodwarf rootstock, only T. harzianum T20a and B. amyloliquefaciens AP4 significantly reduced root rot, but all three isolates significantly reduced leaf fall. For Williams rootstock, all three isolates significantly reduced root rot, but only T. harzianum T20a significantly reduced leaf fall. Thus, the effectiveness of both the Bacillus and Trichoderma isolates was highly dependent upon the pear genotype. The lowest levels of white rot symptoms were observed in the Williams‐T. harzianum T20a interaction resulting in root rot severity of 46.6% and leaf fall of 4.7% at 70 dpi. While the effect of plant genotype on biocontrol activity has been reported frequently for Trichoderma, this is one of the first to report such an effect with a Bacillus biocontrol agent. Both Bacillus and Trichoderma can be effective biocontrol agents of pear white rot, but the plant genotype can have a major impact on their effectiveness.