Many sanitation control problems due to aging facilities and equipment were identified when applying an HACCP system to a flatfish (Paralichthys olivaceus) aquaculture farm. Specifically, the major problems included a lack of awareness about worker hygiene, lack of management of the use of fish medicines, and vulnerability to secondary contamination by cross-contamination owing to a failure to separate breeding tools used for healthy and unhealthy fish. Therefore, the management standards on the farm regarding the surrounding environment, facilities and equipment, breeding tools, feed and medication, and the hygiene of practitioners must be improved. The hygiene management standards were divided into different procedures such as the management of farm hygiene and environmental sanitation, facilities and equipment, fish hygiene, feed, medications, water, and the stocking and shipping of fish. For each procedure, we established the management standards, inspection period, inspection procedures, and how to deal with errors that occur, to enable hygiene management by a small number of managers. Additionally, an inspection system and record form to implement an HACCP system were developed to maintain systematic management. The management and inspection of all aspects of the farm were designed to be easily managed by the supervisor.