The variable regions at the otherwise very conserved WSSV genome can be used to address epidemiological questions. We focused on the relationship between genotype structure of WSSV populations on the one hand and disease outcomes and farming system on the other. We provided evidence that a particular WSSV VNTR structure (in particular the number of repeat units in ORF94) statistically correlate with disease outbreaks and to a lesser extent to farming system. In addition mixed-genotype WSSV infections of shrimp are negatively correlated with disease outbreaks in ponds. It might be possible to use molecular markers (ORF94 and ORF125) to predict the outcome of WSSV infections in shrimp ponds in the future. For shrimp culture, these fi ndings provide important information for the development of specifi c management strategies to control WSD and to advice farmers as to whether to harvest or not.