The soil microbial community is strongly influenced by a wide variety of factors, such as soil characteristics and field management systems. In order to use biological indicators based on microbial community structure, it is very important to know whether or not these factors can be controlled. The present study aimed to determine whether soil type or fertilization has a greater influence on the soil microbial community based on denaturing gradient gel electrophoresis (DGGE) analysis of 12 experimental field plots containing four different soil types, Cumulic Andosol, Low-humic Andosol, Yellow Soil and Gray Lowland Soil, kept under three different fertilizer management systems since 2001 (the application of chemical fertilizer, the application of rice husk and cow manure, and the application of pig manure). Bacterial DGGE analysis using 16S rRNA genes and fungal DGGE analysis using 18S rRNA genes revealed that the bacterial community was related to the soil type more than the fertilization; however, the fungal community was related to the fertilization more than the soil type. These results might suggest that the fungal community is easier to control by fertilization than the bacterial community. Thus, we propose that indicators based on the fungal community might be more suitable as microbial indicators for soil quality.