In recent years, consumers have become much more aware of how diet connects to health. People are increasingly recognizing that functional foods can benefit health when combined with a balanced lifestyle. This growing awareness has boosted demand for foods that support well-being, help people live longer, and reduce disease risk. Enzymatic hydrolysis offers an effective way to use shellfish proteins in many functional food products. This technique often uses methods like membrane filtration or fractionation to refine protein extracts. Bioactive peptides from shellfish proteins do more than supply essential nutrients. They also provide various health benefits. To understand the biological activities of these peptides, researchers need to analyze their specific sequences in detail. This chapter will focus on the processes used to extract, hydrolyze, separate, and identify shellfish proteins. Additionally, it will explore how bioinformatics and molecular simulation can predict the functional properties of shellfish protein peptides.