A pathogenicity assay for in planta screening of biological control agents (BCAs) towards sheath blight in rice was developed, and used to evaluate a panel of Rhizoctonia solani Kuhn hyphae-associated bacteria for their ability to control sheath blight under screenhouse conditions. The best performing BCA, Burkholderia sp. strain A-7.3, was selected for field trials. Disease incidence and disease severity were significantly reduced leading to a significant grain yield increase of 7%. Furthermore, R. solani sclerotia formation and sclerotia viability were significantly reduced, thus lowering the reservoir for primary infections in the next crop cycle. The paper presents a reliable pathogenicity assay that can be used to test BCA performance under different scenarios e.g. plant variety and soil conditions, and help predict translation of results obtained under screenhouse conditions to field performance. Furthermore, it supports the hypothesis that hyphae-associated bacteria are a promising source of niche-specific BCAs towards fungal pathogens.