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Diagnostic molecular genetic markers were developed to estimate the infection frequency following the application of the biocontrol fungusChondrostereum purpureumon two target weed species in a field trial in British Columbia. Sitka alder (Alnus sinuata) and trembling aspen (Populus tremuloides) stump sections were sampled 4 months after treatment with the biocontrol fungus, chemical herbicide, or blank controls and assayed for the presence ofC. purpureum.AChondrostereum-specific PCR primer pair, designed to amplify the intergenic region of ribosomal DNA (rDNA), allowed for the detection ofC. purpureumwhile a second sequence-characterized, amplified region (SCAR) marker was developed to identify the specificC. purpureumgenotypes. Significantly, the biocontrol isolates were recovered only from stumps to which they were applied, suggesting that topical application ofC. purpureumis highly target specific. The absence of secondary infection on control stumps by biocontrol isolates ofC. purpureumindicated that nontarget infection was absent. There was a significant difference in the infection frequencies of the two target weeds. Approximately 90% of biocontrol-treated Sitka alder stems and 40% of trembling aspen stems were successfully infected byC. purpureum.It is expected that this methodology will provide an early indication of success of biocontrol usingC. purpureum.