Regarding the practical farming of Litopenaeus vannamei, the deterioration of water quality from intensive culture systems and environmental pollution is a common but troublesome problem in the cultivation of this species. The toxicities that result from deteriorating water quality, such as that from ammonia stress, have lethal effects on juvenile shrimp and can increase their susceptibility to pathogens. The toxicity of ammonia plays an important role in the frequently high mortality during the early stage on shrimp farms. However, little information is available regarding the genetic parameters of the ammonia tolerance of juveniles in the early stage, but this information is necessary to understand the potential for the genetic improvement of this trait. Considering the euryhalinity of L. vannamei and the fact that low salinity can increase the toxicity of ammonia stress, we estimated the heritability of ammonia tolerance in juveniles in 30‰ (normal) and 5‰ (low) salinity in this study using the survival time (ST) at individual level and the survival status at the half-lethal time (SS50) at the family level. In the normal and low salinity conditions and for the merged data, the heritability estimates of the ST (0.784±0.070, 0.575±0.068, and 0.517±0.058, respectively) and SS50 (0.402±0.061, 0.216±0.050, and 0.264±0.050, respectively) were all significantly greater than zero, which indicates that the ammonia-tolerance of shrimp can be greatly improved. So it might provide an alternative method to reduce mortality, help to enhance resistance to pathogens and reduce the occurrence of infectious diseases. The significant positive genetic correlation between ST and body length suggested that ammonia is more toxic to shrimp in the early stage. The medium-strength genetic correlations of the ST and SS50 between the two environments (0.394±0.097 and 0.377±0.098, respectively) indicate a strong genotype-by-environment (G×E) interaction for ammonia tolerance between the different salinity levels. Therefore, salinity-specific breeding programs for ammonia tolerance in shrimp should be purposefully implemented.