Abstract: We observed the water and sediment in culture ponds for Litopenaeus vannamei in western Guangdong during the rainy season in South China (May~August, 2009) to study the changes of bacterial quantity and microbial diversity index under the influence of severe weather. The results show that the amount of heterotrophic bacteria in water was 104~106 cfumL-1. The amounts of Vibrio exceeded 105 cfumL-1 in the early period, and those were less than 104 cfumL-1 in No.301 and No.404 ponds which were added with probiotics (Bacillus subtilis, etc.) since June 18, while those in No.403 and No.305 ponds often exceeded 105 cfumL-1. In the early period, the ratios of Vibrio to heterotrophic bacteria in water were more than 20% in the 4 ponds, and those were less than 12% in No.301 and No.404 ponds later; in later period, the ratios were 21% and 33% in No.403 and No. 305 ponds, respectively. The amount of heterotrophic bacteria in sediment increased first and then stabilized. The amount of Vibrio in the ponds fluctuated (103~107 cfug-1) except No.305 pond. The microbial community functional diversity index decreased in No.301 and No.404 ponds which were added with probiotics, while that in No.305 and No.403 ponds increased. The diversity index in sediment showed a similar variation, in other words, microbial community richness, dominance of common species and community evenness decreased. The results indicate that applying probiotics periodically in shrimp ponds can stabilizebacterial communities, inhibit growth of Vibrio and reducerisk of micro-ecological environment in case of changeable weather.