The purpose of this study was to explore the structure of the wet market environment and Japanese Mantis Shrimp (JMS) to determine the importance of environmental hygiene in relation to the consumption of raw shrimp. Currently, there is insufficient understanding of the microbiome of JMS and wet market environments. Furthermore, the hygiene maintenance of traditional wet markets in Shantou was found to be below standard, as the holding tanks of JMS were characterized by visible biofilm and murky water. Hence, this study focused on the microbiome of JMS, as well as the biofilm and water sampled inside the holding tank used to store JMS from four wet markets in Shantou City.