This study was designed to improve our understanding of the main causal pathways for white spot disease (WSD) in a representative, 50-pond shrimp farming system in South Sulawesi, Indonesia. The longitudinal observational study focused on recording the occurrence of different genotypes of the causal infectious agent, white spot syndrome virus (WSSV), in selected components of the system across time, and looking for relationships with pond outcomes, particularly WSD occurrence.