Evaluating different rice varieties on fluctuation of beneficial bacteria in a rice-shrimp farming system in Mekong delta, Vietnam was performed in two seasons of 2012-2013. This experiment involved a rotation of wet season rice using hybrid rice variety was compared with the local rice (control treatment), and dry season shrimp culture with Penaeus monodon. The rice fields and shrimp culture techniques were conducted the same management for both systems. It was found that the densities of all bacteria groups gradually increased from the beginning of rice cultivation to the end of shrimp culture, of which the quantities of bacteria in the hybrid rice field were significantly higher than in the control rice field. The densities of bacteria (total bacterial, Bacillus, Nitrosomonas and Nitrobacter) in water and in mud had the peak values at one week before harvesting shrimp, and higher densities of bacteria in the mud compared to those in the pond water. Furthermore, the yield of hybrid rice and its profit were 35% and 92% higher than those for local rice, respectively. Also, rotational culture of P. monodon in the hybrid rice field improved productivity and income as compared to the ones in local rice field. These results indicated that using of hybrid rice in the rice-shrimp farming system not only obtained high yield and profit but also gave favorable conditions for development of beneficial bacteria. This could contribute to the sustainable culture of P. monodon in this system.