Mixed cropping with legume and maize is known as a sustainable agricultural ecosystem because it does not only improve the utilization of fixed-N but also may diversify soil microbial communities due to the different crops’ root-root interaction, but the microbial taxa involving in the diversification were unknown. Thus, we performed a pot study with maize (Zea mays) only treatment and the treatments with maize co-planted with one of two legumes; Mucuna pruriens (L.) DC. (Vel) or Phaseolus vulgaris L. (Com). They were cultivated for 50 days with one of followings; chemical fertilizer (CF), biochar made from chicken manure (CM), or without fertilizer (Ctr). Then, we conducted 16S rRNA analyses to assess soil bacterial diversity. The maize+Vel showed a decrease in the soil microbial diversity after CM application when compared to the Ctr treatment, while the soil with maize+Com showed an increase in the microbial diversity in the same condition (p<0.01). The increase in the relative abundance of treatment specific “rare” taxa was positively related to the increase in microbial diversity, whereas the relative abundance of “dominant” taxa showed the opposite impact. Our experimental result suggested difference in nutrient availability influences the relationship between rare and dominant microbial communities.