White rot on Allium crops recently had a high incidence with increased cultivating areas of tropical garlic types in Korea. Two types of Sclerotium have known as causal agents that produce different size and shapes of sclerotia in infested fields. Therefore, we developed a new method for isolation of sclerotia from infested field soils that can be used for ecological study of Sclerotium spp. and establishment of control strategy. Soil samples collected from heavily infested fields were evenly mixed and placed on a automatic sieve shaker connected with tap water. After 10 min of shaking, residues on 0.5 mm and 0.25 mm sieves were separately collected and suspended with 70% sugar solution, which method floats sclerotia in aqueous layer. Then, floated fraction was carefully separated and mixed with a same volume of 1% sodium hypochlorite solution to differentiate with organic materials. This method provides a direct count of sclerotia under a dissecting microscopy.