The commercial culture of shrimp has expanded rapidly in China in recent decades and is now one of the most important agricultural industries. However, shrimp production decreased significantly between 1992−1997 due to the outbreak of white spot syndrome (WSS). WSS is of serious concern to shrimp farming throughout the world as mortality can approach 100% within 3−10 d of infection with WSSV. There is currently no effective treatment for this disease. We measured the variation in infection intensity of WSSV carried by shrimp (Litopenaeus vannamei) among six ponds in Hongtai Farm in Shanwei of GuangDong province between July and November 2010. In addition, we measured several environmental indices, water quality indicators, and the population structure of planktonic algae. We used real-time PCR to quantify the number WSSV copies in each shrimp. All the shrimp larvae carried WSSV at concentrations ranging from 1.3×103 to 1.7×104 copies/g. Furthermore, the shrimp were infected with WSSV throughout the entire farming period. The mean number of WSSV copies was higher in the gill tissue (2.3×109 copies/g) than in the muscle tissue (3.2×108 copy/g), but the difference was not significant (P>0.05). The number of WSSV copies tended to increase in both tissues throughout the farming period, and was characterized by a number of peaks. During the early rearing period, the number of copies ranged from 1.3×103–3×107copies/g, whereas in the mid and latter stages of rearing the number of copies increased to 1.5×106−1.2×1011 copies/g. In some ponds, outbreaks of WSS forced an end to farming. Rapid changes in water temperature, algae population structure, and weather were also associated with changes in the number of WSSV copies in shrimp. Our results suggest that shrimp can be cultured even when infected with WSSV. The intensity of infection with WSSV varied temporally and was affected by culture time and envi-ronmental factors. We suggest that maintaining the population structure of planktonic algae, keeping water quality constant, and decreasing stress can significantly reduce the likelihood of WSS outbreak.