Early detection of the causative agent which resulted in massive mortalities is a crucial aspect in the health management of shrimp aquaculture. Several diagnostic techniques have been developed for several pathogenic diseases and the use of molecular approaches is widely accepted. The present study optimized published PCR protocols to detect a number of commercially important viral pathogens, including white spot syndrome virus (WSSV), monodon baculovirus (MBV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp as well as to ensure that these PCR assays are suited to Philippine conditions. The optimized PCR protocols for the detection of various viral pathogens in shrimp are sensitive as well as site-specific. These assays can be used as a management tool for the prevention and control of viral diseases in shrimp aquaculture in the country through early detection of the pathogen.