Crustaceans such as prawn and shrimp are nutritious seafood and contain high level of protein. However, due to high-water activity and neutral pH, crustaceans are highly susceptible to spoilage microorganisms that are present as normal microbiota. Development stages and culture environment, diet composition and storage temperature were highlighted in this review as factors that contribute to the composition of microbial communities present in prawn and shrimp. However, the use of biofloc technology during culturing/farming could help to reduce the microbial load at pre-harvest level while the use of neutralized oxidized water could be used to further reduce microbial load during post-harvest handling of the seafood. The use of both biofloc technology and neutral electrolyzed oxidizing water would therefore help to preserve the quality and shelf-life of prawn and shrimp.