Managing stand loss caused by seedling disease (Rhizoctonia solani and other soilborne pathogens) is a challenge in organic rice production because no synthetic fungicides can be used for seed treatment. The use of brassica (mustard) seed meal as a biofumigant to control soilborne pathogens could offer an alternative to seed treatment fungicides. A 2-year study was conducted as a split plot design in a field under organic management to evaluate the performance of mustard seed meal in combination with rice cultivar resistance for reduction in seedling disease. Main plots were soil amendments (mustard seed meal at 1,700 and 3,400 kg/ha, ryegrass green manure, and fallow) and subplots were rice cultivars (Cocodrie, Presidio, and a hybrid). “Pescadero Gold” mustard seed meal and winter annual ryegrass cover crop were incorporated into the soil prior to rice planting. Both mustard seed meal treatments reduced % discolored root area and increased stand compared to fallow and green manure. The hybrid cultivar had a lower % discolored root area and a greater stand than did Cocodrie. Rice yield was greater with the low rate mustard seed meal amendment than with fallow over 2 years. The level of yield was higher in the hybrid than Presidio. Brassica seed meal soil amendment can reduce seedling disease and its combined use with a resistant cultivar such as a hybrid can be an effective approach to reducing stand loss and improving yield under organic production.