Agroecosystem management influences functional biodiversity in cropland fields. A cover-cropping and no-tillage system, recently well-examined practices, is found to affect carbon and nitrogen dynamics in cropland fields. In addition, it is known that these practices keep the soil aggregate structure and thus increases the biodiversity of soil microorganism. Although our knowledge is improved, limited information is available regarding the effects of cover-cropping and tillage system on soil microbial community. Herein, the diversity and dynamics of the microbial communities in upland rice field soils under the agricultural management practices investigated using a molecular genetic technique: an application of real-time quantitative PCR (qPCR) assay to monitor the PCR amplification and then used for terminal-restriction fragment length polymorphisms (T-RFLP) profiling. Analyses of non-metric multidimensional scaling and the rank abundance curve based on the terminal-restriction fragments (T-RFs) profile showed a tiny change of diversity and dynamics of the soil microbial community in the agricultural management practice. These results indicate that soil microbial community flexibly responded to the soil management practice in upland rice field. Moreover, qPCR-T-RFLP profiling provided the database of the soil microbial community in cropland field.