The best method to quantitatively determine populations of Rhizoctonia in soil from soybean fields undergoing rice and soybean rotations was determined for use in a large-scale spatial study to be done over multiple fields and years. The methods evaluated were the toothpick-baiting method, the multiple-pellet soil sampler, and the pour-plate method using elutriated organic matter from soil or surface residue. The toothpick-baiting method was calibrated using the multiple-pellet soil sampler and determined to assay an approximate soil volume of 15.43 cm3. The radius of isolation with the toothpick-baiting technique was approximately 1 cm. In 2009 and 2010, the toothpick method was determined to be the most reliable method for assaying soils, with the most isolates across space and greater recovery of Rhizoctonia solani AG1-IA, R. solani AG11, and R. oryzae, the major Rhizoctonia spp. in these fields, when quantified as propagules per volume of soil or organic matter. In 2011, the recovery of these three groups of Rhizoctonia did not differ statistically when the toothpick-baiting method was compared with the multiple-pellet soil sampler after the volume of soil assayed by the pellet sampler was increased to be similar to that of the toothpick method. However, the labor involved in assaying a similar volume of soil with the multiple-pellet soil sampler was limiting for a large-scale spatial study. The toothpick-baiting method was preferred over the other methods because it was determined to be thorough, inexpensive, nondestructive, and rapid. Additionally, the use of the toothpick-baiting method allows for the determination of the depth of inoculum of isolated fungi for intact soil cores. The mean depth of activity of R. solani AG1-IA, R. solani AG11, and R. oryzae was 1.15, 1.55, and 1.47 cm respectively.