A new and emerging disease is threatening the shrimp industry, a bacterial disease which contains a highly pathogenic plasmid, creating a deadly toxin that causes high mortality in shrimps. The disease has been identified as acute hepatopancreatic necrosis disease (AHPND) or commonly known as early mortality syndrome (EMS). To help the efforts of sustaining the shrimp industry, the study focused on detecting Vibrio parahaemolyticus causing AHPND/EMS affecting Penaeus vannamei (Boone, 1931) (Pacific white shrimp) and Penaeus monodon (Fabricius 1798) (Black Tiger shrimp) in different locations in the Philippines. The presence of the disease was determined by microbiological methods and polymerase chain reaction (PCR) and was confirmed by the histopathology of the hepatopancreas of infected shrimp. Results show that the prevalence of the pathogenic strain of V. parahaemolyticus from the shrimps collected were 33% in Luzon, 21% in Visayas and 5% in Mindanao. The study presents the first record of AHPND/EMS in the country. The detection of this newly emerging disease in the shrimp industry is very crucial as it is the first step in identifying affected sites towards strategizing ways to combat the disease.