The supervision inspection for quality and safety of aquatic seedlings is a task designated by Ministry of Agriculture to improve the quality and safety of aquatic products, in which the sampling procedure serves as a basic link. As many aspects are related in the sampling process such as wide participation of enterprises. Some difficulties may arise for inspection, including diversification of aquatic seedling size, the right time of sampling, the changes of seedling and the difficulties in transportation of aquatic seedling samples. All the above mentioned problems were analyzed in the study and suggestions as to how to improve the situation were put forward.