Nitrogen availability is often one of the limiting factors for intensive rice (Oryza sativa) cultivation. Rotation of rice with upland crops partially reduces nutrient depletion. This study was carried out at CaiLay district, Tien Giang province with the aim to investigate the effect of alternating the rice crop with maize (Zea mays) and mungbean (Phaseolus aureus)in different rotational systems on the diazotrophic community in soilusing pyrosequencing of the nifH genes. The results showed that the community structure of the diazotroph communities in soils were different when rice crop was alternated with either maize or mungbean crop than that in rice monoculture. The nifH sequences were highly diverse and assigned to eleven bacterial phyla and one Archaeal phylum. Proteobacteria and Firmicutes were the most common phyla carrying the nifH gene. The propotion of the Archaea, Betaproteobacteria, Cyanobacteria, Deltaproteobacteria, Firmicutes, Gammaproteobacteria and Nitrospira was significantly different among the treatments. The relative abundances of Anaeromyxobacter, and Geobacter were greater in RRR than in the RMgR treatment while Heliobacterium and Desulfosporosinus were higher in the RMgR than those in the RRR and RMR treatment.