The soil microbial communities and growth of sweet potato are often affected by soil type. This study evaluated the variations in microbial communities of paddy and upland soils used for two sweet potato cultivars (Jinhongmi and Sinjami) cultivation by their fatty acid methyl ester (FAME). The pH, available P 2 O 5 , exchangeable K, Ca, and Mg of upland soil at the harvesting stage were significantly higher than those of paddy soil. The moisture content of paddy soil (28.5%) has increased by 6.7% as compared to upland soil (p < 0.001). The average microbial biomasses in paddy soil were approximately 2.8 times larger for arbuscular mycorrhizal fungi (AMF) and 1.4 -1.6 times larger for fungi, total bacteria, Gram-positive bacteria, total FAMEs, Gram-negative bacteria, and actinomycetes. In addition, The total FAMEs, Gram-positive bacteria, fungi, total bacteria, and AMF in Jinhongmi cultivated soils were significantly larger than those in Sinjami cultivated soils. AMF communities in paddy soil showed significantly larger than that in upland soil (p < 0.001) indicating AMF are potentially responsible for the microbial community differentiation between paddy and upland field. The tuber yield of sweet potato was 28% higher, respectively, in the paddy soil and Sinjami treatment than in the upland soil and Jinhongmi treatment. It was confirmed that the paddy field was more effective on the productivity of sweet potato and soil microbial biomass.