A study expanded pathogen analysis in shrimp using multiple PCR assays and histological examinations, demonstrating that a positive PCR result does not always indicate the actual presence of disease. Frequent coinfections with viruses such as WzSV8 and DHPV, chronic intestinal inflammation, and damage compatible with bacterial toxicity (AHPND) were detected. Microsporidia unrelated to EHP, muscle necrosis, and protozoa in the intestine were also observed. These results highlight the complexity of diseases in farmed shrimp and the need to combine molecular and histological techniques for more accurate diagnosis.