Rice allelopathy has received a great of attention in recent years. Most studies have focused on allelopathic potentials，allelochemicals and trait genes, but few are on interactions between allelopathic rice and soil microbial communities. Actually, soil microbe plays an important role in rice allelopathy in paddy. This study indicated the effect of allelopathic rice variety PI321777 and non-allelopathic rice varieties including “Liaojingjiu" and “Qiuguang" on soil microbial communities in pot culture using spread-plating method or most probable number (MPN). The results showed that allelopathic rice seedlings significantly affected soil microbial communities. Except actinomycete and amonifying bacteria, other microbial numbers in soil growing allelopathic rice seedlings were much less than those of two non-allelopathic rice seedlings. Obvious differences from bacteria, actinomycete, fungi, and aerobic nitrogen-fixing bacteria occurred among these three rice varieties using single factor variance analysis. As a result, allelopathic rice seedlings could significantly reduce the populations of bacteria, actinomycete, fungi, and aerobic nitrogen-fixing bacteria in soil. Allelopathic rice seedlings can release allelochemicals into the soil through root system, and thus, the population reduction of several microbes in soil is probably correlated with the allelochemicals released by allelopathic rice root system. At present, there has been limited success in finding that allelopathic rice interferes with microbial communities in paddy soil. Further research on chemical interactions between allelopathic rice and soil microbe is warranted.