Tropical shrimp aquaculture is facing a disease crisis that may be propelled by an interaction between management practices that cause inbreeding, and the amplification by inbreeding of susceptibility to disease and other stresses. Broodstock accumulate inbreeding and lose genetic diversity when they experience bottlenecks or are chronically too small. The genetic lock is a practice that leads to inbreeding at farm level. Inbreeding may be amplifying the severity of diseases, including the major current threats.