Rice straw transformation takes place in soil but effects of rice straws on relations between soils and bacterial communities of the soils are still poorly understood. PCR and denaturing gradient gelelectrophoresis (DGGE) were used to monitor development of bacterial communities in paddy soil and red soil, into which rice straw or rice straw plus biological agent was applied during incubating period, respectively. The total bacterial DNA from the two studied soils was extracted directly on D0, D5, D25, D45 and D70. The DNA from paddy soil was purified twice, but the DNA from red soil was done only once. The regions V3 of the 16S rDNA of bacteria from the two soils were amplified. DGGE profiles of the PCR productions were compared by similarity analysis. The results show simple DGGE profiles for controls of the two soils without rice straw. Rice straw was incubated in paddy soil and red soil for 70 days. DGGE profiles revealed that the composition of the bacterial community in soil with rice straw was more complex than CK during the incubating period. Meanwhile, the results show that peaks of the bacterial communities appeared at different times in the paddy soil and red soil, treated with rice straw during incubation times.